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Ames, S. K., Gardner, S. N., Marti, J. M., Slezak, T. R., Gokhale, M. B., & Allen, J. E. (2015). Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res., 25(7), 1056–1067.
Abstract: Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.
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Angles-Castillo, A., Perucho, M., Marti, J. M., & Laing, R. A. (2021). On the deceleration of Fanaroff-Riley Class I jets: mass loading of magnetized jets by stellar winds. Mon. Not. Roy. Astron. Soc., 500(1), 1512–1530.
Abstract: In this paper, we present steady-state relativistic magnetohydrodynamic simulations that include a mass-load term to study the process of jet deceleration. The mass load mimics the injection of a proton-electron plasma from stellar winds within the host galaxy into initially pair plasma jets, with mean stellar mass-losses ranging from 10(-14) to 10(-9) M-circle dot yr(-1). The spatial jet evolution covers similar to 500 pc from jet injection in the grid at 10 pc from the jet nozzle. Our simulations use a relativistic gas equation of state and a pressure profile for the ambient medium. We compare these simulations with previous dynamical simulations of relativistic, non-magnetized jets. Our results show that toroidal magnetic fields can prevent fast jet expansion and the subsequent embedding of further stars via magnetic tension. In this sense, magnetic fields avoid a runaway deceleration process. Furthermore, when the mass load is large enough to increase the jet density and produce fast, differential jet expansion, the conversion of magnetic energy flux into kinetic energy flux (i.e. magnetic acceleration), helps to delay the deceleration process with respect to non-magnetized jets. We conclude that the typical stellar population in elliptical galaxies cannot explain jet deceleration in classical Fanaroff-Riley type I radio galaxies. However, we observe a significant change in the jet composition, thermodynamical parameters, and energy dissipation along its evolution, even for moderate values of the mass load.
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Dorado-Morales, P., Vilanova, C., Pena-Garay, C., Marti, J. M., & Porcar, M. (2015). Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling. Sci Rep, 5, 18396–6pp.
Abstract: We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia.
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