ABSTRACT
BACKGROUND: Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. This allows for easy combination of various data analysis, modeling and simulation methods. RESULTS: This article presents major functionalities introduced into Biotite since its original publication. The fields of application are shown using concrete examples. We show that the computational performance of Biotite for bioinformatics tasks is comparable to individual, special purpose software systems specifically developed for the respective single task. CONCLUSIONS: The results show that Biotite can be used as program library to either answer specific bioinformatics questions and simultaneously allow the user to write entire, self-contained software applications with sufficient performance for general application.
Subject(s)
Computer Simulation , Models, Molecular , Proteins , Software , Programming Languages , Sequence Alignment , Base Sequence , Proteins/chemistry , alpha-Globins/chemistry , HumansABSTRACT
BACKGROUND: Most experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds. RESULTS: We present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used. CONCLUSIONS: We bundled the algorithm into the open-source Python package and command line program Hydride. Since usually no additional parametrization is necessary for the problem at hand, the software works out-of-box for a wide range of molecular systems usually within a few seconds of computation time. Hence, we believe that Hydride could be a valuable tool for structural biologists and biophysicists alike.
ABSTRACT
The main objective of the present paper is to report on the concentration of silicon carbide (SiC) fibres, crystalline silica and respirable dust in a Canadian SiC production plant and to compare the results with earlier investigations. The second objective is to tentatively explain the differences in concentration of the fibrogenic substances between different countries. The assessment of SiC fibres, dusts, respirable quartz and cristobalite was performed according to standard procedures. The highest 8 h time-weighted average concentrations of fibres were found among the crusher and backhoe attendants and the carboselectors with an arithmetic mean of 0.63 fibres ml(-1) for the former group and 0.51 fibres ml(-1) for the latter group. The results of respirable SiC fibres in the Canadian plant were lower than in the Norwegian and Italian industries. Most of the 8 h time-weighted average concentrations for quartz were less than or around the limit of detection of 0.01 mg m(-3). The maximum 8 h time-weighted average concentration for quartz was found among the carboselectors (0.157 mg m(-3)), followed by the labourers (0.032 mg m(-3)). Similarly, most of the 8 h time-weighted average cristobalite measurements were less than the limit of detection of 0.01 mg m(-3) except for the carboselectors where it was found to be 0.044 mg m(-3). The assessment of the Italian occupational settings exposure demonstrated elevated quartz concentrations, while cristobalite was absent. The authors have concluded that the investigations that were performed in the last two decades in this field by researchers from different countries seem to support that SiC fibres (whiskers) constitute a major airborne health hazard.
Subject(s)
Air Pollutants, Occupational/analysis , Carbon Compounds, Inorganic , Dust , Occupational Exposure/analysis , Quartz , Silicon Compounds , Silicon Dioxide , Canada , Chemical Industry , Environmental Monitoring/methods , Humans , Italy , Mineral Fibers/analysis , Norway , Particle SizeABSTRACT
El Programa de Prevención Secundaria y Terciaria del alcoholismo en el nivel Primario de atención de salud del SSMS se efectúa en los 19 Consultorios Periféricos a cargo del equipo de salud general, conformado por médico, asistente social y enfermera. La coordinación la efectúa el Programa de las Personas y el DAP del SSMS en conjunto con la Comisión Asesora de Salud Mental, compuesta por los autores de este trabajo. Que, además, asesora, supervisa y capacita al equipo de salud de los Consultorios Periféricos y coordina al nivel primario con los niveles secundarios (Servicios de Psiquiatría del Hospital Barros Luco-Trudeau) y terciarios (Hospital Sanatorio El Peral). Se presenta la evaluación del Programa de Alcoholismo de los 470 pacientes ingresados a él en el Primer Semestre de 1983 que han sido seguidos hasta el 30.06.85. Se efectuá cinco cortes evaluativos al 30.06.83; 31.12.83; 30.06.84; 31.12.84 y 30.06.85. Se compara la evolución de los 8 indicadores utilizados en los cortes: abstinencia, recaída, inasistencia, abandono, referencia, traslado, muerte y alta. Al 30.06.85 en el 42.96% de los 470 pacientes ha fracasado el tratamiento. Tienen recaída (1.91%), inasistencia (9.14%) o han abandonado (31.91%). El 21.27% han sido referidos a atención secundaria (4.46%) o han sido trasladados 16.81%) a otras áreas del país. Han muerto el 5.53%. El 30.85% restantes están abstinentes (14.04% o han sido dados de alta 16.17%). Al excluir el rubro otros egresos (referencia, traslado y muerte), y corregir sobre el nuevo total, los tramientos exitosos (abstinencia y alta) significan el 41.27%
