"Assessment of band-based similarity coefficients for Type/Subtype classification in Pulsed Field Gel Electrophoresis using ROC curves."

Pulsed-field gel electrophoresis has been the microbial typing method of choice for strain identification in epidemiological studies of several bacterial species with medical importance such as Staphylococcus aureus , Streptococcus pneumoniae , Escherichia coli, and many others. The usual procedures for the comparison of strains and assignment for strain type and subtype is visual assessment of number band differences and/or using software for band detection and using band-based similarity coefficients such as Dice or Jaccard. For both methods the classification decision is based on a pre-defined threshold level, selected based on the clustering pattern displayed on the dendrogram containing the strains of interest. In this paper we propose a method of evaluating the classification power of different band based similarity coefficients on a given strain collection using Receiving Operating Characteristic (ROC) Curves, and we tested the effect on band position tolerance on Bionumerics T software on the proposed classification.

"Relative Volatility, Evolution and Transcription."

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"Understanding the Prooxidative Mechanisms of Superoxide Dismutase."

Superoxide Dismutase (SOD) is an enzyme that protects cells from oxidative stress by keeping the cellular concentration of the superoxide anion radical at very low levels. Albeit the irrefutable evidences that SOD is essential for aerobic life, a growing body of evidence has shown that elevated SOD activities can lead to deleterious effects. Yet, the mechanisms underlying these observations remain unclear. Some have suggested that the adverse effects of high SOD activities are due to an increase in the product of the reaction catalysed by SOD - hydrogen peroxide - whereas others have proposed that excessive superoxide depletion may inhibit important physiological processes in which this radical species may be involved. By analysing biochemical models using a mathematical approach we were able to show that both hypotheses are correct and identified the physiological conditions in which either type of mechanism (i.e., involving superoxide or hydrogen peroxide) may be the main contributer to the adverse effects of high SOD activities. When applying the same tools to a specific model of ischemia-reperfusion injury where the prooxidative effects of high SOD activities have also been observed, we find that excessive depletion of superoxide is most likely the mechanisms involved in the observed toxicity. Several alternative mechanisms are proposed that can be experimentally tested.

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Measles is a disease caused by a highly contagious virus which infects only human beings. The disease may be complicated by a number of illnesses and remains a worldwide health problem. In Portugal, before vaccination, virtually everybody was infected at least once in a lifetime and epidemics took place every 2 to 3 years. Before the introduction of antibiotics, the number of annual deaths by measles reached 162 per million individuals. Vaccination against measles was introduced in the Portuguese National Programme of Vaccination (PNV) in 1974. The infection remained endemic, exhibiting seasonal peaks every March to May, but the inter-epidemic period enlarged to 4-5 years and mortality was greatly reduced to 0-5 deaths/year/million individuals. Long-lasting vaccination programmes worldwide confirm the theoretical prediction that it is practically impossible to eliminate measles with a single dose of the vaccine given on a routine basis. Thus in 1990 Portugal introduced a second dose of the vaccine in the PNV. I investigate theoretical conditions for the elimination of measles with n (n > 1) doses of the vaccine. For the particular case of n = 2 doses, it can be shown that a high vaccination coverage in the first dose remains crucial for elimination. The existence of a second dose, however, places elimination at the reach of the Portuguese PNV. The vaccination coverage in Portugal was investigated and shown to have been quite variable. Apparently, conditions were never met in Portugal for measles elimination with routine vaccination alone. Measles dynamics in Portugal has been influenced by multiple factors which are dificult to incorporate into simple mathematical models with analytical solutions. Such factors include vaccination campaigns, routine vaccination at dierent rates, seasonal aggregation of hosts, transmission coe cients dependent on age, etc. In order to account for these factors, a simulation model is presented which reproduces the qualitative and, to a certain extent, quantitative dynamics of measles in Portugal. The model is thus a useful tool to examine the consequences of changes in factors underlying the disease dynamics. Using the model, I have identified the critical year when the number of newborns from mothers immunized by the vaccine, exceeds the number of newborns from mothers infected by the wild virus. In that year, it might be appropriate to antecipate the age recommended for administration of the first dose of the vaccine against measles.