rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrodinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge.net/

A correlation sensitivity analysis of non-life underwriting risk in solvency capital requirement estimation

This paper analyses the impact of using different correlation assumptions between lines of business when estimating the risk-based capital reserve, the Solvency Capital Requirement -SCR-, under Solvency II regulations. A case study is presented and the SCR is calculated according to the Standard Model approach. Alternatively, the requirement is then calculated using an Internal Model based on a Monte Carlo simulation of the net underwriting result at a one-year horizon, with copulas being used to model the dependence between lines of business. To address the impact of these model assumptions on the SCR we conduct a sensitivity analysis. We examine changes in the correlation matrix between lines of business and address the choice of copulas. Drawing on aggregate historical data from the Spanish non-life insurance market between 2000 and 2009, we conclude that modifications of the correlation and dependence assumptions have a significant impact on SCR estimation.

Implementació d'un ERP open source amb programació a mida

This work presents, from the perspective of a freelancer professional, a case study of a practical and real implementation of an Open Source ERP software suite to a very small company, including the development of a custom software module to adapt the suite to the particular needs of the company.

Servei de rutes basat en Open Source Routing Machine

Aquesta memòria descriu la preparació, l'execució i els resultats obtinguts d'implementar un sistema calculador de rutes. El projecte Open Source Routing Machine és un motor calculador de rutes d'alt rendiment que utilitza les dades de OpenStreetMaps per calcular el camí més curt entre dos punts. En aquest projecte final no únicament es volen utilitzar les dades OpenStreetMap sinó que també es pretenen utilitzar dades pròpies en format shapefile i poder visualitzar-los en un visor web. Aquest visor permet a l'usuari, de forma senzilla, sol•licitar rutes al servidor OSRM creat, obtenint la ruta desitjada en molt pocs milisegons

Comparative effects of macro-sized aluminum oxide and aluminum oxide nanoparticles on erythrocyte hemolysis: influence of cell source, temperature and size

Al2O3 is the most abundantly produced nanomaterial and has been used in diverse fields, including the medical, military and industrial sectors. As there are concerns about the health effects of nanoparticles, it is important to understand how they interact with cells, and specifically with red blood cells. The hemolysis induced by three commercial nano-sized aluminum oxide particles (nanopowder 13 nm, nanopowder <50 nm and nanowire 2-6 nm × 200-400 nm) was compared to aluminum oxide and has been studied on erythrocytes from humans, rats and rabbits, in order to elucidate the mechanism of action and the influence of size and shape on hemolytic behavior. The concentrations inducing 50% hemolysis (HC50) were calculated for each compound studied. The most hemolytic aluminum oxide particles were of nanopowder 13, followed by nanowire and nanopowder 50. The addition of albumin to PBS induced a protective effect on hemolysis in all the nano-forms of Al2O3, but not on Al2O3. The drop in HC50 correlated to a decrease in nanomaterial size, which was induced by a reduction of aggregation Aluminum oxide nanoparticles are less hemolytic than other oxide nanoparticles, and behave differently depending on the size and shape of the nanoparticles. The hemolytic behavior of aluminum oxide nanoparticles differs from that of aluminum oxide.

Estimation of Water Circulation in a Mediterranean Salt Marsh and its Relationship with Flooding Causes

Variations in water volume in small depressions in Mediterranean salt marshes in Girona (Spain) are described and the potential causes for these variations analysed. Although the basins appear to be endorrheic, groundwater circulation is intense, as estimated from the difference between water volume observed and that expected from the balance precipitation / evaporation. The rate of variation in volume (VR = AV / VAt) may be used to estimate groundwater supply ('circulation'), since direct measurements of this parameter are impossible. Volume.conductivity figures can also be used to estimate the quantity of circulation, and to investigate the origin of water supplied to the system. The relationships between variations in the volume of water in the basins and the main causes of flooding are also analysed. Sea storms, rainfall levels and strong, dry northerly winds are suggested as the main causes of the variations in the volumes of basins. The relative importance assigned to these factors has changed, following the recent regulation of freshwater flows entering the system

Estimation of age- and stage-specific Catalan breast cancer survival functions using US and Catalan survival data

During the last part of the 1990s the chance of surviving breast cancer increased. Changes in survival functions reflect a mixture of effects. Both, the introduction of adjuvant treatments and early screening with mammography played a role in the decline in mortality. Evaluating the contribution of these interventions using mathematical models requires survival functions before and after their introduction. Furthermore, required survival functions may be different by age groups and are related to disease stage at diagnosis. Sometimes detailed information is not available, as was the case for the region of Catalonia (Spain). Then one may derive the functions using information from other geographical areas. This work presents the methodology used to estimate age- and stage-specific Catalan breast cancer survival functions from scarce Catalan survival data by adapting the age- and stage-specific US functions. Methods: Cubic splines were used to smooth data and obtain continuous hazard rate functions. After, we fitted a Poisson model to derive hazard ratios. The model included time as a covariate. Then the hazard ratios were applied to US survival functions detailed by age and stage to obtain Catalan estimations. Results: We started estimating the hazard ratios for Catalonia versus the USA before and after the introduction of screening. The hazard ratios were then multiplied by the age- and stage-specific breast cancer hazard rates from the USA to obtain the Catalan hazard rates. We also compared breast cancer survival in Catalonia and the USA in two time periods, before cancer control interventions (USA 1975–79, Catalonia 1980–89) and after (USA and Catalonia 1990–2001). Survival in Catalonia in the 1980–89 period was worse than in the USA during 1975–79, but the differences disappeared in 1990–2001. Conclusion: Our results suggest that access to better treatments and quality of care contributed to large improvements in survival in Catalonia. On the other hand, we obtained detailed breast cancer survival functions that will be used for modeling the effect of screening and adjuvant treatments in Catalonia

Comparative effects of macro-sized aluminum oxide and aluminum oxide nanoparticles on erythrocyte hemolysis: influence of cell source, temperature and size

Al2O3 is the most abundantly produced nanomaterial and has been used in diverse fields, including the medical, military and industrial sectors. As there are concerns about the health effects of nanoparticles, it is important to understand how they interact with cells, and specifically with red blood cells. The hemolysis induced by three commercial nano-sized aluminum oxide particles (nanopowder 13 nm, nanopowder <50 nm and nanowire 2-6 nm × 200-400 nm) was compared to aluminum oxide and has been studied on erythrocytes from humans, rats and rabbits, in order to elucidate the mechanism of action and the influence of size and shape on hemolytic behavior. The concentrations inducing 50% hemolysis (HC50) were calculated for each compound studied. The most hemolytic aluminum oxide particles were of nanopowder 13, followed by nanowire and nanopowder 50. The addition of albumin to PBS induced a protective effect on hemolysis in all the nano-forms of Al2O3, but not on Al2O3. The drop in HC50 correlated to a decrease in nanomaterial size, which was induced by a reduction of aggregation Aluminum oxide nanoparticles are less hemolytic than other oxide nanoparticles, and behave differently depending on the size and shape of the nanoparticles. The hemolytic behavior of aluminum oxide nanoparticles differs from that of aluminum oxide.