NGS metabarcoding proves successful for quantitative assessment of symbiont abundance: the case of feather mites on birds.

Understanding the ecological function of species and the structure of communities is crucial in the study of ecological interactions among species. For this purpose, not only the occurrence of particular species but also their abundance in ecological communities is required. However, abundance quantification of species through morphological characters is often difficult or time/money consuming when dealing with elusive or small taxa. Here we tested the use of next-generation sequencing (NGS) for abundance estimation of two species of feather mites (Proctophyllodes stylifer and Pteronyssoides parinus) under five proportions (16:1, 16:4, 16:16, 16:64, and 16:256 mites) against a mock community composed by Proctophyllodes clavatus and Proctophyllodes sylviae. In all mixtures, we retrieved sequence reads from all species. We found a strong linear relationship between 454 reads and the real proportion of individuals in the mixture for both focal species. The slope for Pr. stylifer was close to one (0.904), and the intercept close to zero (-0.007), thus showing an almost perfect correspondence between real and estimated proportions. The slope for Pt. parinus was 0.351 and the intercept 0.307, showing that while the estimated proportion increased linearly relative to real proportions of individuals in the samples, proportions were overestimated at low real proportions and underestimated at larger ones. Additionally, pyrosequencing replicates from each DNA extraction were highly repeatable (R = 0.920 and 0.972, respectively), showing that the quantification method is highly consistent given a DNA extract. Our study suggests that NGS is a promising tool for abundance estimation of feather mites' communities in birds.

Formation of spikes and bubbles in the linear phase of Rayleigh-Taylor instability in elastic-plastic media.

The generation of spikes and bubbles, a typical characteristic of the nonlinear regime in the Rayleigh-Taylor instability, is found to occur as well during the linear regime in an elastic-plastic solid medium caused, however, by a very different mechanism. This singular feature originates in the differential loads at different locations of the interface, which makes that the transition from the elastic to the plastic regime takes place at different times, thus producing an asymmetric growth of peaks and valleys that rapidly evolves in exponentially growing spikes, while bubbles can also grow exponentially at a lower rate.

Partition of Omega-like facility into two configurations of 24 and 36 laser beams to improve implosion performance.

An Omega-like beam configuration is considered where the 60-beam layout can be separated into two independent sub-configurations with 24 and 36 laser beams, each minimizing direct drive illumination non-uniformity. Two different laser focal spot profiles, one associated with each configuration, are proposed to apply the zooming technique in order to increase the laser-target coupling efficiency. This approach is used by 1D hydrodynamics simulations of the implosion of a direct-drive capsule characterized by a relatively large aspect ratio A = 7 and an optimized laser pulse shape delivering a maximum of 30 TW and 30 kJ, with different temporal pulse shapes in each of the two sets of beams. It is shown that zooming allows for an optimistic 1D thermonuclear energy gain greater than one while without zooming the thermonuclear gain remains largely below one. While this is incompatible with the as-built Omega laser, it provides a promising option for a future intermediate-energy direct drive laser system.

Two-dimensional simulations of Rayleigh-Taylor instability in elastic-plastic media.

Two-dimensional numerical simulations for the Rayleigh-Taylor instability in an elastic-plastic medium are presented. Recent predictions of the theory regarding the asymmetric growth of peaks and valleys during the linear phase of the instability evolution are confirmed. Extension to the nonlinear regime reveals singular features, such as the long delay in achieving the nonlinear saturation and an intermediate phase with growth rate larger than the classical one.

Cylindrical convergence effects on the Rayleigh-Taylor instability in elastic and viscous media.

Convergence effects on the perturbation growth of an imploding surface separating two nonideal material media (elastic and viscous media) are analyzed in the case of a cylindrical implosion in both the Rayleigh-Taylor stable and unstable configurations. In the stable configuration, the perturbation damping effect due to angular momentum conservation becomes destroyed for sufficiently high values of the elastic modulus or of the viscosity of the media. For the unstable configuration, Rayleigh-Taylor instability can be suppressed by the elasticity or mitigated by the viscosity, but without practically affecting the perturbation growth due to the geometrical convergence. However, the convergence effects manifest themselves in a manner somewhat different from the classical Bell-Plesset effect by making the process more sensitive to the media compressibility than in the case involving ideal media.

Elastic-plastic Rayleigh-Taylor instability at a cylindrical interface.

The boundaries of stability are determined for the Rayleigh-Taylor instability at a cylindrical interface between an ideal fluid in the interior and a heavier elastic-plastic solid in the outer region. The stability maps are given in terms of the maximum dimensionless initial amplitude ξ_{th}^{*} that can be tolerated for the interface to remain stable, for any particular value of the dimensionless radius B of the surface, and for the different spatial modes m of the perturbations. In general, for the smallest dimensionless radius and larger modes m, the interface remains stable for larger values of ξ_{th}^{*}. In particular, for m>1 and B→0, it turns out ξ_{th}^{*}→1, and a cylindrical geometry equivalent to Drucker's criterion is found, which indeed ends up being independent of the interface geometry.

Rayleigh-Taylor instability in elastic-plastic solid slabs bounded by a rigid wall.

The linear evolution of the incompressible Rayleigh-Taylor instability for the interface between an elastic-plastic slab medium and a lighter semi-infinite ideal fluid beneath the slab is developed for the case in which slab is attached to a rigid wall at the top surface. The theory yields the maps for the stability in the space determined by the initial perturbation amplitude and wavelength, as well as for the transition boundary from the elastic to the plastic regimes for arbitrary thicknesses of the slab and density contrasts between the media. In particular, an approximate but very accurate scaling law is found for the minimum initial perturbation amplitude required for instability and for the corresponding perturbation wavelength at which it occurs. These results allows for an interpretation of the recent experiments by Maimouni et al. [Phys. Rev. Lett. 116, 154502 (2016)PRLTAO0031-900710.1103/PhysRevLett.116.154502].

Studies of equation of state properties of high-energy-density matter generated by intense ion beams at the facility for antiprotons and ion research.

The work presented in this paper shows with the help of two-dimensional hydrodynamic simulations that intense heavy-ion beams are a very efficient tool to induce high energy density (HED) states in solid matter. These simulations have been carried out using a computer code BIG2 that is based on a Godunov-type numerical algorithm. This code includes ion beam energy deposition using the cold stopping model, which is a valid approximation for the temperature range accessed in these simulations. Different phases of matter achieved due to the beam heating are treated using a semiempirical equation-of-state (EOS) model. To take care of the solid material properties, the Prandl-Reuss model is used. The high specific power deposited by the projectile particles in the target leads to phase transitions on a timescale of the order of tens of nanosecond, which means that the sample material achieves thermodynamic equilibrium during the heating process. In these calculations we use Pb as the sample material that is irradiated by an intense uranium beam. The beam parameters including particle energy, focal spot size, bunch length, and bunch intensity are considered to be the same as the design parameters of the ion beam to be generated by the SIS100 heavy-ion synchrotron at the Facility for Antiprotons and Ion Research (FAIR), at Darmstadt. The purpose of this work is to propose experiments to measure the EOS properties of HED matter including studies of the processes of phase transitions at the FAIR facility. Our simulations have shown that depending on the specific energy deposition, solid lead will undergo phase transitions leading to an expanded hot liquid state, two-phase liquid-gas state, or the critical parameter regime. In a similar manner, other materials can be studied in such experiments, which will be a very useful addition to the knowledge in this important field of research.

Utility of lateral flow tests in SARS-CoV-2 infection monitorization.

OBJECTIVE: The diagnosis of SARS-CoV-2 infection is crucial for medical and public health reasons, to allow the best treatment of cases and the best control of the pandemic. Serology testing allows for the detection of asymptomatic infections and 19-COVID cases once the virus has been cleared. We analyzed the usefulness of the SARS-CoV-2 rapid test of Autobio and tried to correlate its pattern with the severity of COVID19 infection. METHODS: We analyzed the accuracy and clinical usefulness of a point-of-care IgM and/or IgG test for SARS-CoV-2 in 35 COVID-19 patients [12 (34.3%) mild-moderate and 23 (65.7%) severe-critical] admitted to a field hospital in Madrid, as well as in 5 controls. RESULTS: The mean time from the first day of symptoms to the antibody test was 28 days (SD: 8.7), similar according to the severity of the disease. All patients with SARS-CoV-2 PCR+ showed the corresponding IgG positivity, while these results were negative in all control individuals. A total of 26 (74%) cases also presented with positive IgM, 19 (83%) were severe-critical cases and 7 (58%) were mild-moderate cases. The IgM response lasted longer in the severe critical cases (mean: 29.7 days; SD: 8.4) compared to the moderate cases (mean: 21.2 days; SD: 2.0).. CONCLUSIONS: Rapid serology tests are useful for the diagnosis of patients with COVID-19 (mainly IgG detection) and may also be correlated with the severity of the infection (based on IgM detection).

Large Hadron Collider at CERN: Beams generating high-energy-density matter.

This paper presents numerical simulations that have been carried out to study the thermodynamic and hydrodynamic responses of a solid copper cylindrical target that is facially irradiated along the axis by one of the two Large Hadron Collider (LHC) 7 TeV/ c proton beams. The energy deposition by protons in solid copper has been calculated using an established particle interaction and Monte Carlo code, FLUKA, which is capable of simulating all components of the particle cascades in matter, up to multi-TeV energies. These data have been used as input to a sophisticated two-dimensional hydrodynamic computer code BIG2 that has been employed to study this problem. The prime purpose of these investigations was to assess the damage caused to the equipment if the entire LHC beam is lost at a single place. The FLUKA calculations show that the energy of protons will be deposited in solid copper within about 1 m assuming constant material parameters. Nevertheless, our hydrodynamic simulations have shown that the energy deposition region will extend to a length of about 35 m over the beam duration. This is due to the fact that first few tens of bunches deposit sufficient energy that leads to high pressure that generates an outgoing radial shock wave. Shock propagation leads to continuous reduction in the density at the target center that allows the protons delivered in subsequent bunches to penetrate deeper and deeper into the target. This phenomenon has also been seen in case of heavy-ion heated targets [N. A. Tahir, A. Kozyreva, P. Spiller, D. H. H. Hoffmann, and A. Shutov, Phys. Rev. E 63, 036407 (2001)]. This effect needs to be considered in the design of a sacrificial beam stopper. These simulations have also shown that the target is severely damaged and is converted into a huge sample of high-energy density (HED) matter. In fact, the inner part of the target is transformed into a strongly coupled plasma with fairly uniform physical conditions. This work, therefore, has suggested an additional very important application of the LHC, namely, studies of HED states in matter.

Stability boundaries for the Rayleigh-Taylor instability in accelerated elastic-plastic solid slabs.

The linear theory of the incompressible Rayleigh-Taylor instability in elastic-plastic solid slabs is developed on the basis of the simplest constitutive model consisting in a linear elastic (Hookean) initial stage followed by a rigid-plastic phase. The slab is under the action of a constant acceleration, and it overlays a very thick ideal fluid. The boundaries of stability and plastic flow are obtained by assuming that the instability is dominated by the average growth of the perturbation amplitude and neglecting the effects of the higher oscillation frequencies during the stable elastic phase. The theory yields complete analytical expressions for such boundaries for arbitrary Atwood numbers and thickness of the solid slabs.

Richtmyer-Meshkov instability in elastic-plastic media.

An analytical model for the linear Richtmyer-Meshkov instability in solids under conditions of high-energy density is presented, in order to describe the evolution of small perturbations at the solid-vacuum interface. The model shows that plasticity determines the maximum perturbation amplitude and provides simple scaling laws for it as well as for the time when it is reached. After the maximum amplitude is reached, the interface remains oscillating with a period that is determined by the elastic shear modulus. Extensive two-dimensional simulations are presented that show excellent agreement with the analytical model. The results suggest the possibility to experimentally evaluate the yield strength of solids under dynamic conditions by using a Richtmyer-Meshkov-instability-based technique.

Linear Rayleigh-Taylor instability in an accelerated Newtonian fluid with finite width.

The linear theory of Rayleigh-Taylor instability is developed for the case of a viscous fluid layer accelerated by a semi-infinite viscous fluid, considering that the top interface is a free surface. Effects of the surface tensions at both interfaces are taken into account. When viscous effects dominate on surface tensions, an interplay of two mechanisms determines opposite behaviors of the instability growth rate with the thickness of the heavy layer for an Atwood number A_{T}=1 and for sufficiently small values of A_{T}. In the former case, viscosity is a less effective stabilizing mechanism for the thinnest layers. However, the finite thickness of the heavy layer enhances its viscous effects that, in general, prevail on the viscous effects of the semi-infinite medium.

Finite-thickness effects on the Rayleigh-Taylor instability in accelerated elastic solids.

A physical model has been developed for the linear Rayleigh-Taylor instability of a finite-thickness elastic slab laying on top of a semi-infinite ideal fluid. The model includes the nonideal effects of elasticity as boundary conditions at the top and bottom interfaces of the slab and also takes into account the finite transit time of the elastic waves across the slab thickness. For Atwood number A_{T}=1, the asymptotic growth rate is found to be in excellent agreement with the exact solution [Plohr and Sharp, Z. Angew. Math. Mech. 49, 786 (1998)10.1007/s000330050121], and a physical explanation is given for the reduction of the stabilizing effectiveness of the elasticity for the thinner slabs. The feedthrough factor is also calculated.

Rayleigh-Taylor instability in accelerated elastic-solid slabs.

We develop the linear theory for the asymptotic growth of the incompressible Rayleigh-Taylor instability of an accelerated solid slab of density ρ_{2}, shear modulus G, and thickness h, placed over a semi-infinite ideal fluid of density ρ_{1}<ρ_{2}. It extends previous results for Atwood number A_{T}=1 [B. J. Plohr and D. H. Sharp, Z. Angew. Math. Phys. 49, 786 (1998)ZAMPA80044-227510.1007/s000330050121] to arbitrary values of A_{T} and unveil the singular feature of an instability threshold below which the slab is stable for any perturbation wavelength. As a consequence, an accelerated elastic-solid slab is stable if ρ_{2}gh/G≤2(1-A_{T})/A_{T}.

Richtmyer-Meshkov flow in elastic solids.

Richtmyer-Meshkov flow is studied by means of an analytical model which describes the asymptotic oscillations of a corrugated interface between two perfectly elastic solids after the interaction with a shock wave. The model shows that the flow stability is due to the restoring effect of the elastic force. It provides a simple approximate but still very accurate formula for the oscillation period. It also shows that as it is observed in numerical simulations, the amplitude oscillates around a mean value equal to the post-shock amplitude, and that this is a consequence of the stress free conditions of the material immediately after the shock interaction. Extensive numerical simulations are presented to validate the model results.

Rayleigh-Taylor instability in elastic solids.

We present an analytical model for the Rayleigh-Taylor instability that allows for an approximate but still very accurate and appealing description of the instability physics in the linear regime. The model is based on the second law of Newton and it has been developed with the aim of dealing with the instability of accelerated elastic solids. It yields the asymptotic instability growth rate but also describes the initial transient phase determined by the initial conditions. We have applied the model to solid/solid and solid/fluid interfaces with arbitrary Atwood numbers. The results are in excellent agreement with previous models that yield exact solutions but which are of more limited validity. Our model allows for including more complex physics. In particular, the present approach is expected to lead to a more general theory of the instability that would allow for describing the transition to the plastic regime.

Hydrodynamic instability of elastic-plastic solid plates at the early stage of acceleration.

A model is presented for the linear Rayleigh-Taylor instability taking place at the early stage of acceleration of an elastic-plastic solid, when the shock wave is still running into the solid and is driven by a time varying pressure on the interface. When the the shock is formed sufficiently close to the interface, this stage is considered to follow a previous initial phase controlled by the Ritchmyer-Meshkov instability that settles new initial conditions. The model reproduces the behavior of the instability observed in former numerical simulation results and provides a relatively simpler physical picture than the currently existing one for this stage of the instability evolution.

Implosion of multilayered cylindrical targets driven by intense heavy ion beams.

An analytical model for the implosion of a multilayered cylindrical target driven by an intense heavy ion beam has been developed. The target is composed of a cylinder of frozen hydrogen or deuterium, which is enclosed in a thick shell of solid lead. This target has been designed for future high-energy-density matter experiments to be carried out at the Gesellschaft für Schwerionenforschung, Darmstadt. The model describes the implosion dynamics including the motion of the incident shock and the first reflected shock and allows for calculation of the physical conditions of the hydrogen at stagnation. The model predicts that the conditions of the compressed hydrogen are not sensitive to significant variations in target and beam parameters. These predictions are confirmed by one-dimensional numerical simulations and thus allow for a robust target design.