RESUMEN
Mass transport in bulk spinel ferrites NiFe2O4 is studied computationally using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo algorithm. Diffusion mechanisms-difficult to observe with molecular dynamics-are described by k-ART. Point defects are assumed to be responsible for ionic diffusion; thus, both cation and anion defects are investigated. This work focuses on vacancies and interstitials by comparing their properties with two Buckingham potential parameterizations: one with nominal charges and the other with partial charges. Both potentials are corrected at short distances, thus allowing interstitial diffusion and avoiding the catastrophic infinite energies appearing with Buckingham at short distances. The energy landscape along different pathways is described in detail. Both potentials predict the same mechanisms but different migration energies. Mechanisms by which a normal spinel is transformed to an inverse spinel via cation diffusion are unveiled, and diffusion coefficients are predicted. We find that interstitial Ni diffusion involves the movement of two Ni ions and that O interstitials trigger a collective diffusion of O ions, while an O vacancy diffuses by an O ion moving to the center of a cuboctahedron.
RESUMEN
OBJECTIVES: Establishing a correlation between the number of HTLV-1 provirus and the characteristics of the genomic environment in ATL cases. METHODOLOGY: A systematic search was made of publications as well as a meta-analysis of the pertinent literature considering proviruses per chromosome and structural and functional characteristics of flanking chromatin regions as variables. The concordance of experts' study was evaluated by Spearman Rho correlation. Publication bias was analysed by funnel plot and the Egger statisgrapher. A fixed effects model was applied according to heterogeneity evaluation to combine the results of integration occurring in coding sequences as well as coding sequences according to their molecular function. RESULTS: The expert concepts' Kappa index was 0.7 and no publication bias was observed. The meta-analysis result was homogeneous (p>0.05). HTLV-1 integration was directed towards several chromosomes' telomeric and subtelomeric regions. The combination of published results in the articles which were analysed supported the hypothesis of integration events being site-directed towards coding regions of the human genome (p<0.05). Moreover, the groups of genes having enzymatic and receptor functions was statistically significant. CONCLUSION: The results led to concluding that HTLV-I integration in the ATLL cases analysed here was not random but was directed towards regulatory regions. Such results could help to explain the role of some processes involved in leukemogenesis.
Asunto(s)
Virus Linfotrópico T Tipo 1 Humano/genética , Leucemia-Linfoma de Células T del Adulto/virología , Integración Viral , Adulto , Biología Computacional , Virus Linfotrópico T Tipo 1 Humano/fisiología , Humanos , Leucemia-Linfoma de Células T del Adulto/epidemiología , Leucemia-Linfoma de Células T del Adulto/genéticaRESUMEN
Objetivos Establecer la relación entre el número de provirus VLHT-1 y las características de la cromatina adyacente en casos de Leucemia Linfoma de Células T del Adulto. Metodología Se realizó una revisión sistemática y un metaanálisis de la literatura publica que considero como variables de estudio los provirus por cromosoma y características estructurales y funcionales de la cromatina adyacente a los sitios de integración. La concordancia entre los resultados de la evaluación que emitieron dos expertos fue evaluada con el coeficiente de Spearman Rho. Se evaluó el sesgo de publicación mediante el gráfico de embudo y el estadígrafo Egger. De acuerdo con los resultados de la evaluación de la heterogeneidad se aplicó el modelo de efectos fijos para la combinación de los resultados de las integraciones que ocurrieron en: secuencias codificantes y secuencias codificantes de acuerdo con su función molecular. Resultados La concordancia entre expertos evaluadores fue de 0,7. No se encontró sesgo de publicación. Se determinó homogeneidad entre los estudios seleccionados (p>0,05). El provirus VLHT-1 se integró en secuencias en regiones teloméricas y subteloméricas. La combinación de los resultados mostró una integración sitio dirigida hacia regiones codificantes del genoma humano (p<0,05). Conclusión En su conjunto los resultados permiten concluir que la integración proviral no es al azar en LCCTA; ésta ocurrió en regiones reguladoras o de control; que explicarían algunos de los proceso moleculares involucrado en leukomogénesis.
Objectives Establishing a correlation between the number of HTLV-1 provirus and the characteristics of the genomic environment in ATL cases. Methodology A systematic search was made of publications as well as a meta-analysis of the pertinent literature considering proviruses per chromosome and structural and functional characteristics of flanking chromatin regions as variables. The concordance of experts' study was evaluated by Spearman Rho correlation. Publication bias was analysed by funnel plot and the Egger statisgrapher. A fixed effects model was applied according to heterogeneity evaluation to combine the results of integration occurring in coding sequences as well as coding sequences according to their molecular function. Results The expert concepts' Kappa index was 0.7 and no publication bias was observed. The meta-analysis result was homogeneous (p>0.05). HTLV-1 integration was directed towards several chromosomes' telomeric and subtelomeric regions. The combination of published results in the articles which were analysed supported the hypothesis of integration events being site-directed towards coding regions of the human genome (p<0.05). Moreover, the groups of genes having enzymatic and receptor functions was statistically significant. Conclusion The results led to concluding that HTLV-I integration in the ATLL cases analysed here was not random but was directed towards regulatory regions. Such results could help to explain the role of some processes involved in leukemogenesis.