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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Olmo, G. J., & Rubiera-Garcia, D. (2015). The quantum, the geon and the crystal. Int. J. Mod. Phys. D, 24(9), 1542013–15pp.
Abstract: Effective geometries arising from a hypothetical discrete structure of spacetime can play an important role in the understanding of the gravitational physics beyond General Relativity (GR). To discuss this question, we make use of lessons from crystalline systems within solid state physics, where the presence of defects in the discrete microstructure of the crystal determine the kind of effective geometry needed to properly describe the system in the macroscopic continuum limit. In this work, we study metric-affine theories with nonmetricity and torsion, which are the gravitational analog of crystalline structures with point defects and dislocations. We consider a crystal-motivated gravitational action and show the presence of topologically nontrivial structures (wormholes) supported by an electromagnetic field. Their existence has important implications for the quantum foam picture and the effective gravitational geometries. We discuss how the dialogue between solid state physics systems and modified gravitational theories can provide useful insights on both sides.
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Pavez, C., Pedreros, J., Tarifeño-Saldivia, A., & Soto, L. (2015). Observation of plasma jets in a table top plasma focus discharge. Phys. Plasmas, 22(4), 040705–5pp.
Abstract: In the last years, medium size Z-pinch experiments operating at tens of kJ are being used to create supersonic plasma jets. Those experiments are produced with wire arrays and radial foils, and they are conducted in generators based on water-filled transmission lines. Also plasma jets have been observed in small X-pinch experiments operating at 1 kJ. In this work, observations of plasma jets produced in a table top plasma focus device by means of optical and digital interferometry are shown. The device was operated at only similar to 70J, achieving 50 kA in 150 ns. The plasma jets were observed after the pinch, in the region close and on the anode, along the axis. The electron density measured from the jets is in the range 10(24)-10(25) m(-3). From two consecutive plasma images separated 18 ns, the axial jet velocity was measured in the order of 4 x 10(4) m/s.
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Cauchi, M., Assmann, R. W., Bertarelli, A., Carra, F., Lari, L., Rossi, A., et al. (2015). Thermomechanical assessment of the effects of a jaw-beam angle during beam impact on Large Hadron Collider collimators. Phys. Rev. Spec. Top.-Accel. Beams, 18(2), 021001–14pp.
Abstract: The correct functioning of a collimation system is crucial to safely and successfully operate high-energy particle accelerators, such as the Large Hadron Collider (LHC). However, the requirements to handle high-intensity beams can be demanding, and accident scenarios must be well studied in order to assess if the collimator design is robust against possible error scenarios. One of the catastrophic, though not very probable, accident scenarios identified within the LHC is an asynchronous beam dump. In this case, one (or more) of the 15 precharged kicker circuits fires out of time with the abort gap, spraying beam pulses onto LHC machine elements before the machine protection system can fire the remaining kicker circuits and bring the beam to the dump. If a proton bunch directly hits a collimator during such an event, severe beam-induced damage such as magnet quenches and other equipment damage might result, with consequent downtime for the machine. This study investigates a number of newly defined jaw error cases, which include angular misalignment errors of the collimator jaw. A numerical finite element method approach is presented in order to precisely evaluate the thermomechanical response of tertiary collimators to beam impact. We identify the most critical and interesting cases, and show that a tilt of the jaw can actually mitigate the effect of an asynchronous dump on the collimators. Relevant collimator damage limits are taken into account, with the aim to identify optimal operational conditions for the LHC.
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Cauchi, M., Assmann, R. W., Bertarelli, A., Carra, F., Cerutti, F., Lari, L., et al. (2015). Thermomechanical response of Large Hadron Collider collimators to proton and ion beam impacts. Phys. Rev. Spec. Top.-Accel. Beams, 18(4), 041002–14pp.
Abstract: The CERN Large Hadron Collider (LHC) is designed to accelerate and bring into collision high-energy protons as well as heavy ions. Accidents involving direct beam impacts on collimators can happen in both cases. The LHC collimation system is designed to handle the demanding requirements of high-intensity proton beams. Although proton beams have 100 times higher beam power than the nominal LHC lead ion beams, specific problems might arise in case of ion losses due to different particle-collimator interaction mechanisms when compared to protons. This paper investigates and compares direct ion and proton beam impacts on collimators, in particular tertiary collimators (TCTs), made of the tungsten heavy alloy INERMET (R) 180. Recent measurements of the mechanical behavior of this alloy under static and dynamic loading conditions at different temperatures have been done and used for realistic estimates of the collimator response to beam impact. Using these new measurements, a numerical finite element method (FEM) approach is presented in this paper. Sequential fast-transient thermostructural analyses are performed in the elastic-plastic domain in order to evaluate and compare the thermomechanical response of TCTs in case of critical beam load cases involving proton and heavy ion beam impacts.
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