19 research outputs found
Thermal photons in QGP and non-ideal effects
We investigate the thermal photon production-rates using one dimensional
boost-invariant second order relativistic hydrodynamics to find proper time
evolution of the energy density and the temperature. The effect of
bulk-viscosity and non-ideal equation of state are taken into account in a
manner consistent with recent lattice QCD estimates. It is shown that the
\textit{non-ideal} gas equation of state i.e behaviour
of the expanding plasma, which is important near the phase-transition point,
can significantly slow down the hydrodynamic expansion and thereby increase the
photon production-rates. Inclusion of the bulk viscosity may also have similar
effect on the hydrodynamic evolution. However the effect of bulk viscosity is
shown to be significantly lower than the \textit{non-ideal} gas equation of
state. We also analyze the interesting phenomenon of bulk viscosity induced
cavitation making the hydrodynamical description invalid. We include the
viscous corrections to the distribution functions while calculating the photon
spectra. It is shown that ignoring the cavitation phenomenon can lead to
erroneous estimation of the photon flux.Comment: 11 pages, 13 figures; accepted for publication in JHE
Infectious hematopoietic necrosis virus (IHNV) persistence in Sockeye Salmon: influence on brain transcriptome and subsequent response to the viral mimic poly(I:C)
Stringent response of Escherichia coli: revisiting the bibliome using literature mining
Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologically relevant concepts in free text, namely genes, tRNAs, mRNAs, gene products and small molecules, is crucial to capture the structure and functioning of different responses.
Results
In this work, we review literature reports on the study of the stringent response in Escherichia coli. Rather than undertaking the development of a highly specialised literature mining approach, we investigate the suitability of concept recognition and statistical analysis of concept occurrence as means to highlight the concepts that are most likely to be biologically engaged during this response. The co-occurrence analysis of core concepts in this stringent response, i.e. the (p)ppGpp nucleotides with gene products was also inspected and suggest that besides the enzymes RelA and SpoT that control the basal levels of (p)ppGpp nucleotides, many other proteins have a key role in this response. Functional enrichment analysis revealed that basic cellular processes such as metabolism, transcriptional and translational regulation are central, but other stress-associated responses might be elicited during the stringent response. In addition, the identification of less annotated concepts revealed that some (p)ppGpp-induced functional activities are still overlooked in most reviews.
Conclusions
In this paper we applied a literature mining approach that offers a more comprehensive analysis of the stringent response in E. coli. The compilation of relevant biological entities to this stress response and the assessment of their functional roles provided a more systematic understanding of this cellular response. Overlooked regulatory entities, such as transcriptional regulators, were found to play a role in this stress response. Moreover, the involvement of other stress-associated concepts demonstrates the complexity of this cellular response