The Rainbow Prim Algorithm for Selecting Putative Orthologous Protein Sequences

We present a selection method designed for eliminating species redundancy in clusters of putative orthologous sequences, to be applied as a post-processing procedure to pre-clustered data obtained from other methods. The algorithm can always zero-out the cluster redundancy while preserving the number of species of the original cluster

High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment

Bioinformatics applications are naturally distributed, due to distribution of involved data sets, experimental data and biological databases. They require high computing power, owing to the large size of data sets and the complexity of basic computations, may access heterogeneous data, where heterogeneity is in data format, access policy, distribution, etc., and require a secure infrastructure, because they could access private data owned by different organizations. The Problem Solving Environment (PSE) is an approach and a technology that can fulfil such bioinformatics requirements. The PSE can be used for the definition and composition of complex applications, hiding programming and configuration details to the user that can concentrate only on the specific problem. Moreover, Grids can be used for building geographically distributed collaborative problem solving environments and Grid aware PSEs can search and use dispersed high performance computing, networking, and data resources. In this work, the PSE solution has been chosen as the integration platform of bioinformatics tools and data sources. In particular an experiment of multiple sequence alignment on large scale, supported by the LIBIPSE, is presented

Large scale analysis of protein stability in OMIM disease related human protein variants

Modern genomic techniques allow to associate several Mendelian human diseases to single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears to assume a particular relevance in annotating whether a single residue substitution can or cannot be associated to a given disease. Thermodynamic properties of human proteins and of their disease related variants are lacking. In the present work, we take advantage of the available three dimensional structure of human proteins for predicting the role of disease related variations on the perturbation of protein stability

On the statistical evaluation of dose-response functions

The linear-quadratic dependence of effect on the dose of ionizing radiation and its biophysical implications are considered. The estimation of the parameters of the response function and the derivation of the joint confidence region of the estimates are described. The method is applied to the induction of pink mutations inTradescantia which follows the linear-quadratic model. The statistical procedure is also suitable for other response functions

I moti frumentari ad Alghero nel 1821: cronaca di una sommossa popolare

En els dies 25, 26 i 27 de març de 1821 va haver-hi a l'Alguer una insurrecció popular: l’escassesa del pa i la pujada dels preus havien ja alimentat un greu malcontent i el 25 de març els rebels van bloquejar les naus carregades de blat per a la venda a ultramar del comerciant Esteve Piccinelli i obligant alhora el Governador Di Suni a fer-ne descarregar el preciós aliment. El dia següent el malcontent es transforma en una veritable insurrecció i els rebels, capitanejats pels germans Canelles ("Caneglias"), saquejaren els magatzems deis comerciants més rics. Víctimes innocents del furor popular foren el mercader Caieta Rossi i la seva filia Annamarb, assassinats bàrbarament. El 27 de març la insurrecció es va aplacar i 75 persones foren arrestades. El procés instruït poc després, com demostra en apèndix la sentencia, es conclogué amb nombroses condemnes capitals i moltes amb la cadena perpètua

Inhibition of nitric oxide biosynthesis by anthocyanin fraction of blackberry extract.

Anthocyanins are natural colorant belonging to the flavonoid family, widely distributed among flowers, fruits, and vegetables. Some flavonoids have been found to possess anticarcinogenic, cytotoxic, cytostatic, antioxidant, and anti-inflammatory properties. Since increased nitric oxide (NO) plays a role in inflammation, we have investigated whether the pharmacological activity of the anthocyanin fraction of a blackberry extract (cyanidin-3-O-glucoside representing about 88% of the total anthocyanin content) was due to the suppression of NO synthesis. The markedly increased production of nitrites by stimulation of J774 cells with lipopolysaccharide (LPS) for 24 h was concentration-dependently inhibited by the anthocyanin fraction (11, 22, 45, and 90 μg/ml) of the extract. Moreover, this inhibition was dependent on a dual mechanism, since the extract attenuated iNOS protein expression and decreased the iNOS activity in lungs from LPS-stimulated rats. Inhibition of iNOS protein expression appeared to be at the transcriptional level, since the extract and similarly cyanidin-3-O-glucoside (10, 20, 40, and 80 μg/ml, amounts corresponding to the concentrations present in the extract) decreased LPS-induced NF-κB activation, through inhibition of IκBα degradation, and reduced ERK-1/2 phosphorylation in a concentration-dependent manner. In conclusion, our study demonstrates that at least some part of the anti-inflammatory activity of blackberry extract is due to the suppression of NO production by cyanidin-3-O-glucoside, which is the main anthocyanin present in the extract. The mechanism of this inhibition seems to be due to an action on the expression/activity of the enzyme. In particular, the protein expression was inhibited through the attenuation of NF-κB and/or MAPK activatio

Is Gun Crime Learned? Social Learning Theory and Guns

This study examines the relationship between specific childhood experiences and the use of guns in crime in a sample of incarcerated males in American prisons. Two specific childhood experiences are examined: exposure to violence in the home and exposure to guns in the home. Utilizing social learning theory, I argue that adult male felons who used guns in the commission of crimes will have had greater levels of exposure to violence and exposure to guns in their childhood home. Using a data set collected by sociologists James Wright and Peter Rossi, I conducted a binary logistic regression to determine the existence and strength of relationships between the variables. Results show that exposure to violence, as defined in this study, did not predict adult criminal gun usage, but that exposure to guns, and the control variable of race do predict adult criminal gun usage. I then address the limitations of the study and the implications of these findings for the furtherance of social learning theory as well as suggest directions for future research on gun violence