Identification of plasmodium vivax proteins with potential role in invasion using sequence redundancy reduction and profile hidden markov models

Background: This study describes a bioinformatics approach designed to identify Plasmodium vivax proteins potentially involved in reticulocyte invasion. Specifically, different protein training sets were built and tuned based on different biological parameters, such as experimental evidence of secretion and/or involvement in invasion-related processes. A profile-based sequence method supported by hidden Markov models (HMMs) was then used to build classifiers to search for biologically-related proteins. The transcriptional profile of the P. vivax intra-erythrocyte developmental cycle was then screened using these classifiers. Results: A bioinformatics methodology for identifying potentially secreted P. vivax proteins was designed using sequence redundancy reduction and probabilistic profiles. This methodology led to identifying a set of 45 proteins that are potentially secreted during the P. vivax intra-erythrocyte development cycle and could be involved in cell invasion. Thirteen of the 45 proteins have already been described as vaccine candidates; there is experimental evidence of protein expression for 7 of the 32 remaining ones, while no previous studies of expression, function or immunology have been carried out for the additional 25. Conclusions: The results support the idea that probabilistic techniques like profile HMMs improve similarity searches. Also, different adjustments such as sequence redundancy reduction using Pisces or Cd-Hit allowed data clustering based on rational reproducible measurements. This kind of approach for selecting proteins with specific functions is highly important for supporting large-scale analyses that could aid in the identification of genes encoding potential new target antigens for vaccine development and drug design. The present study has led to targeting 32 proteins for further testing regarding their ability to induce protective immune responses against P. vivax malaria.

Neighborhood characteristics and the spatial concentration of crime: Evidence for Bogotá

Using a unique neighborhood crime dataset for Bogotá in 2011, this study uses a spatial econometric approach and examines the role of socioeconomic and agglomeration variables in explaining the variance of crime. It uses two different types of crime, violent crime represented in homicides and property crime represented in residential burglaries. These two types of crime are then measured in non-standard crime statistics that are created as the area incidence for each crime in the neighborhood. The existence of crime hotspots in Bogotá has been shown in most of the literature, and using these non-standard crime statistics at this neighborhood level some hotspots arise again, thus validating the use of a spatial approach for these new crime statistics. The final specification includes socioeconomic, agglomeration, land-use and visual aspect variables that are then included in a SARAR model an estimated by the procedure devised by Kelejian and Prucha (2009). The resulting coefficients and marginal effects show the relevance of these crime hotspots which is similar with most previous studies. However, socioeconomic variables are significant and show the importance of age, and education. Agglomeration variables are significant and thus more densely populated areas are correlated with more crime. Interestingly, both types of crimes do not have the same significant covariates. Education and young male population have a different sign for homicide and residential burglaries. Inequality matters for homicides while higher real estate valuation matters for residential burglaries. Finally, density impacts positively both crimes.