Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

Residential property loans and performance during property price booms: evidence from European banks

Understanding the performance of banks is of the utmost relevance, because of the impact of this sector on economic growth and financial stability. Of all the different assets that make up a bank portfolio, the residential mortgage loans constitute one of its main. Using the dynamic panel data method, we analyse the influence of residential mortgage loans on bank profitability and risk, using a sample of 555 banks in the European Union (EU-15), over the period from 1995 to 2008. We find that banks with larger weights of residential mortgage loans show lower credit risk in good times. This result explains why banks rush to lend on property during booms due to the positive effects it has on credit risk. The results show further that credit risk and profitability are lower during the upturn in the residential property price cycle. The results also reveal the existence of a non-linear relationship (U-shaped marginal effect), as a function of bank’s risk, between profitability and the residential mortgage loans exposure. For those banks that have high credit risk, a large exposure of residential mortgage loans is associated with higher risk-adjusted profitability, through lower risk. For banks with a moderate/low credit risk, the effects of higher residential mortgage loan exposure on its risk-adjusted profitability are also positive or marginally positive.

Residential property loans and performance during property price booms: evidence from European

Understanding the performance of banks is of the u tmost importance due to the impact the sector may have on economic growth and financial stability. Residential mortgage loans constitute a large proportion of the portfolio of many banks and are one of the key assets in the determination of performance. Using a dynamic panel model , we analyse the impact of res idential mortgage loans on bank profitability and risk , based on a sample of 555 banks in the European Union ( EU - 15 ) , over the period from 1995 to 2008. We find that banks with larger weight s in residential mortgage loans display lower credit risk in good market conditions . This result may explain why banks rush to lend on property during b ooms due to the positive effect it has on credit risk . The results also show that credit risk and profitability are lower during the upturn in the residential property cy cle. Furthermore, t he results reveal the existence of a non - linear relationship ( U - shaped marginal effect), as a function of bank’s risk, between profitability and residential mortgage exposure . For those banks that have high er credit risk, a large exposur e to residential loans is associated with increased risk - adjusted profitability, through a reduction in risk. For banks with a moderate to low credit risk, the impact of higher exposure are also positive on risk - adjusted profitability.

Evidence of long-term changes in the distribution of key intertidal species

World Congress of Malacology, Ponta Delgada, July 22-28, 2013.

Habitat differentiation between groups of Risso's dolphins as evidence of coastal nursery areas

26th Annual Conference of the European Cetacean Society, Galway, Ireland 26-28 March 2012.

QoS em WIMAX – Análise e avaliação de módulos para simulação com o ns-2

Mestrado em Engenharia Electrotécnica e de Computadores

Demand response in future power systems management – a conceptual framework and simulation tool

Mestrado em Engenharia Electrotécnica – Sistemas Eléctricos de Energia

Deep ocean species. The little that is known mostly comes from collected specimens. Comment on L.A. Rocha et al. Letter "Specimen collection: An essential tool" (23 May, 344: 814).

Deep Ocean Species. The little that is known mostly comes from collected specimens. L.A. Rocha et al. Letter "Specimen collection: An essential tool" (23 May, 344: 814) brilliantly discuss the importance of specimen collection and present the evolution of collecting since the mid-19th century until our present strict codes and conducts. However, it is also important to emphasize the fact that the vast majority of deep ocean macro-organisms are only known to us because of collection and this is a strong argument that should be present in our actions as scientists. If the deep is considered the least known of Earth’s habitats (1% or so according to recent estimates) then what awesome collection of yet to discover species are still there to be properly described? As the authors point citing (1), something around 86% of species remain unknown. Voucher specimens are fundamental for the reasons pointed out and perhaps the vast depths of the World’s oceans are the best example of that importance. The resumed report of 2010 Census of Marine Life (2) showed that among the millions of specimens collected in both familiar and seldom-explored waters, the Census found more than 6,000 potentially new species and completed formal descriptions of more than 1,200 of them. It also found that a number of rare species are in fact common. Voucher specimens are essential and, again agreeing with L.A. Rocha et al. Letter (see above), the modern approach for collecting will not be a cause for extinctions but instead a valuable tool for knowledge, description and even, as seen above, a way to find out that supposed rare species may not be that rare and even prove to reach abundant populations.

Estudo e análise de soluções de acessos Wimax partilhados em cenários residenciais

Mestrado em Engenharia Electrotécnica e de Computadores

An ultrasound based computer-aided diagnosis tool for steatosis detection

Liver steatosis is a common disease usually associated with social and genetic factors. Early detection and quantification is important since it can evolve to cirrhosis. In this paper, a new computer-aided diagnosis (CAD) system for steatosis classification, in a local and global basis, is presented. Bayes factor is computed from objective ultrasound textural features extracted from the liver parenchyma. The goal is to develop a CAD screening tool, to help in the steatosis detection. Results showed an accuracy of 93.33%, with a sensitivity of 94.59% and specificity of 92.11%, using the Bayes classifier. The proposed CAD system is a suitable graphical display for steatosis classification.

The gambin model provides a superior fit to species abundance distributions with a single free parameter : evidence, implementation and interpretation

The species abundance distribution (SAD) has been a central focus of community ecology for over fifty years, and is currently the subject of widespread renewed interest. The gambin model has recently been proposed as a model that provides a superior fit to commonly preferred SAD models. It has also been argued that the model's single parameter (α) presents a potentially informative ecological diversity metric, because it summarises the shape of the SAD in a single number. Despite this potential, few empirical tests of the model have been undertaken, perhaps because the necessary methods and software for fitting the model have not existed. Here, we derive a maximum likelihood method to fit the model, and use it to undertake a comprehensive comparative analysis of the fit of the gambin model. The functions and computational code to fit the model are incorporated in a newly developed free-to-download R package (gambin). We test the gambin model using a variety of datasets and compare the fit of the gambin model to fits obtained using the Poisson lognormal, logseries and zero-sum multinomial distributions. We found that gambin almost universally provided a better fit to the data and that the fit was consistent for a variety of sample grain sizes. We demonstrate how α can be used to differentiate intelligibly between community structures of Azorean arthropods sampled in different land use types. We conclude that gambin presents a flexible model capable of fitting a wide variety of observed SAD data, while providing a useful index of SAD form in its single fitted parameter. As such, gambin has wide potential applicability in the study of SADs, and ecology more generally.

The evidence of conventional physiotherapeutic interventions after exercise-induced muscle damage: systematic review and meta-analysis

Abstract Introduction: Exhaustive and/or unaccustomed exercise, mainly those involving eccentric muscle actions, induces temporary muscle damage, evidenced by Delayed Onset Muscle Soreness. Different strategies to recover the signs and symptoms of this myogenic condition have been studied by researchers, as a result a significant number of articles on this issue have been published. Purpose: A systematic review was conducted to assess the evidence of the physiotherapeutic interventions of exercise-induced muscle damage. Methods: The electronic data bases were searched, including MEDLINE (1996-2011), CINHAL (1982- 2011), EMBASE (1988-2011), PEDro (1950-2011), and SPORTDiscus (1985-2011). Systematic review was limited to randomized control trials (RCTs) studies, written in English or Portuguese, which included physiotherapeutic interventions, namely massage, cryotherapy, stretching and low-intensity exercise, on adult human subjects (18-60 years old) of either gender. Studies were excluded when the intervention could not be assessed independently. The methodological quality of RCTs was independently assessed with the PEDro Scale by three reviewers. Results: Thirty-three studies were included in the systematic review; eight analyzed the effects of the massage, ten analyzed the effects of the cryotherapy, eight the effect of stretching and seventeen focused low-intensity exercise intervention. The results suggest that massage is the most effective intervention and that there is inconclusive evidence to support the use of cryotherapy; whereas the other conventional, namely stretching and low-intensity exercise, there is no evidence to prove their efficacy. Conclusion: The results allow the conclusion that massage is the physiotherapeutic intervention that demonstrated to be the most effective in the relief of symptoms and signs of exercise-induced muscle damage, as a result, massage should still be used in the muscular recovery after sports activities.

Interoperabilidade ferroviária: infraestrutura (Bitola)

Dissertação para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

A new multiplexed microsatellite tool for metapopulation studies in the overexploited endemic limpet Patella aspera (Röding, 1798)

Patellid limpets are ecologically important keystone grazers having a long history of overexploitation in the Macaronesian Archipelagos (NE Atlantic islands), where some species, such as Patella aspera, are under serious risk.[1, 2] Patella aspera is a protandric sequential hermaphrodite species with external fertilization, in which individuals start off as males but may undergo a sex reversal with age.[3] Hence, exploitation tends to focus on the larger females in the population as larger limpets (predominantly females) are selectively removed. Despite conservation legislation in Canaries, Madeira and Azores, limpets are under severe pressure and few individuals survive long enough to become females, a phenomenon that severely restricts the effective population size.[4] New conservation actions for the protection and sustainable use of limpets in Macaronesian Archipelagos are urgently needed and should be based on a multidisciplinary framework based on knowledge of the population dynamics and connectivity of this species.