Periodic gravity-capillary waves on a fluid of finite depth with constant vorticity are studied theoretically and numerically. The classical Stokes expansion method is applied to obtain the wave profile and the interior flow up to the fourth order of approximation, which thereby extends the works of Barakat & Houston (1968) J. Geophys. Res. 73 (20), 6545–6554 and Hsu et al. (2016) Proc. R. Soc. Lond. A 472, 20160363. The classical perturbation scheme possesses singularities for certain wavenumbers, whose variations with depth are shown to be affected by the vorticity. This analysis also reveals that for any given value of the physical depth, there exists a threshold value of the vorticity above which there are no singularities in the theoretical solution. The validity of the third- and fourth-order solutions is examined by comparison with exact numerical results, which are obtained with a method based on conformal mapping and Fourier series expansions of the wave surface. The outcomes of this comparison are surprising as they report important differences in the internal flow structure, when compared with the third-order predictions, even though both approximations predict almost perfectly the phase velocity and the surface profiles. Usually, this occurs when the wavenumber is far enough from a critical value and the steepness is not too large. In these non-resonant cases, it is found that the fourth-order theory is more consistent with the exact numerical results. With negative vorticity the improvement is noticeable both beneath the crest and the trough, whereas with positive vorticity the fourth-order theory does a better job either beneath the crest or beneath the trough, depending of the type of the wave.

In submerged sandy slopes, soil is frequently eroded as a combination of two main mechanisms: breaching, which refers to the retrogressive failure of a steep slope forming a turbidity current, and instantaneous sliding wedges, known as shear failure, that also contribute to shape the morphology of the soil deposit. Although there are several modes of failures, in this paper we investigate breaching and shear failures of granular columns using the two-fluid approach. The numerical model is first applied to simulate small-scale granular column collapses (Rondon et al., Phys. Fluids, vol. 23, 2011, 073301) with different initial volume fractions to study the role of the initial conditions in the main flow dynamics. For loosely packed granular columns, the porous medium initially contracts and the resulting positive pore pressure leads to a rapid collapse. Whereas in initially dense-packing columns, the porous medium dilates and negative pore pressure is generated stabilizing the granular column, which results in a slow collapse. The proposed numerical approach shows good agreement with the experimental data in terms of morphology and excess of pore pressure. Numerical results are extended to a large-scale application (Weij, doctoral dissertation, 2020, Delft University of Technology; Alhaddad et al., J. Mar. Sci. Eng., vol. 11, 2023, 560) known as the breaching process. This phenomenon may occur naturally at coasts or on dykes and levees in rivers but it can also be triggered by humans during dredging operations. The results indicate that the two-phase flow model correctly predicts the dilative behaviour and the subsequent turbidity currents associated with the breaching process.

The optimal timing of blood culture (BCx) sets collection has not been evaluated with continuous BCx detection systems. The yield of BCx was similar between short intervals (median, 3 minutes) and longer intervals (median, 16 or 43 minutes) among 5,856 BCx, except for improved polymicrobial bacteremia detection with long-interval BCx.

In, essentially, all species where meiotic crossovers (COs) have been studied, they occur preferentially in open chromatin, typically near gene promoters and to a lesser extent, at the end of genes. Here, in the case of Arabidopsis thaliana, we unveil further trends arising when one considers contextual information, namely summarised epigenetic status, gene or intergenic region size, and degree of divergence between homologs. For instance, we find that intergenic recombination rate is reduced if those regions are less than 1.5 kb in size. Furthermore, we propose that the presence of single nucleotide polymorphisms enhances the rate of CO formation compared to when homologous sequences are identical, in agreement with previous works comparing rates in adjacent homozygous and heterozygous blocks. Lastly, by integrating these different effects, we produce a quantitative and predictive model of the recombination landscape that reproduces much of the experimental variation.

When a deposited layer of granular material fully immersed in a liquid is suddenly inclined above a certain critical angle, it starts to flow down the slope. The initial dynamics of these underwater avalanches strongly depends on the initial volume fraction. If the granular bed is initially loose, i.e. looser than the critical state, the avalanche is triggered almost instantaneously and exhibits a strong acceleration, whereas for an initially dense granular bed, i.e. denser than the critical state, the avalanche's mobility remains low for some time before it starts flowing normally. This behaviour can be explained by a combination of geometrical granular dilatancy and pore pressure feedback on the granular media. In this contribution, a continuum formulation is presented and implemented in a three-dimensional continuum numerical model. The originality of the present model is to incorporate dilatancy as an elasto-plastic normal stress or pressure and not as a modification of the friction coefficient. This allows an explanation of the two different behaviours of initially loose and dense underwater avalanches. It also highlights the contribution from each depth-resolved variable in the strongly coupled transition to a flowing avalanche. The model compares favourably with existing experiments for the initiation of underwater granular avalanches. Results reveal the interplay between shear-induced changes of the granular stress and fluid pressure in the dynamics of avalanches. The characteristic time of the triggering phase is nearly independent of the local rheological parameters, whereas the initial drop in pore pressure and the surface velocity at steady state still strongly depend on them. Finally, the multidimensional capabilities of the model are illustrated for the two-dimensional Hele-Shaw configuration and some of the observed differences between one-dimensional simulations and experiments are clarified.

We present experimental data providing evidence for the formation of transient (${\sim }20\ \mathrm {\mu }\textrm {s}$) plasmas that are simultaneously weakly magnetized (i.e. Hall magnetization parameter $\omega \tau > 1$) and dominated by thermal pressure (i.e. ratio of thermal-to-magnetic pressure $\beta > 1$). Particle collisional mean free paths are an appreciable fraction of the overall system size. These plasmas are formed via the head-on merging of two plasmas launched by magnetized coaxial guns. The ratio $\lambda _{\textrm {gun}}=\mu _0 I_{\textrm {gun}}/\psi _{\textrm {gun}}$ of gun current $I_{\textrm {gun}}$ to applied magnetic flux $\psi _{\textrm {gun}}$ is an experimental knob for exploring the parameter space of $\beta$ and $\omega \tau$. These experiments were conducted on the Big Red Ball at the Wisconsin Plasma Physics Laboratory. The transient formation of such plasmas can potentially open up new regimes for the laboratory study of weakly collisional, magnetized, high-$\beta$ plasma physics; processes relevant to astrophysical objects and phenomena; and novel magnetized plasma targets for magneto-inertial fusion.

Although testing is widely regarded as critical to fighting the COVID-19 pandemic, what measure and level of testing best reflects successful infection control remains unresolved. Our aim was to compare the sensitivity of two testing metrics – population testing number and testing coverage – to population mortality outcomes and identify a benchmark for testing adequacy. We aggregated publicly available data through 12 April on testing and outcomes related to COVID-19 across 36 OECD (Organization for Economic Development) countries and Taiwan. Spearman correlation coefficients were calculated between the aforementioned metrics and following outcome measures: deaths per 1 million people, case fatality rate and case proportion of critical illness. Fractional polynomials were used to generate scatter plots to model the relationship between the testing metrics and outcomes. We found that testing coverage, but not population testing number, was highly correlated with population mortality (rs = −0.79, P = 5.975 × 10−9 vs. rs = −0.3, P = 0.05) and case fatality rate (rs = −0.67, P = 9.067 × 10−6 vs. rs = −0.21, P = 0.20). A testing coverage threshold of 15–45 signified adequate testing: below 15, testing coverage was associated with exponentially increasing population mortality; above 45, increased testing did not yield significant incremental mortality benefit. Taken together, testing coverage was better than population testing number in explaining country performance and can serve as an early and sensitive indicator of testing adequacy and disease burden.

The bifurcation of two-dimensional gravity–capillary waves into solitary waves when the phase velocity and group velocity are nearly equal is investigated in the presence of constant vorticity. We found that gravity–capillary solitary waves with decaying oscillatory tails exist in deep water in the presence of vorticity. Furthermore we found that the presence of vorticity influences strongly (i) the solitary wave properties and (ii) the growth rate of unstable transverse perturbations. The growth rate and bandwidth instability are given numerically and analytically as a function of the vorticity.

All organisms encounter pathogens, and birds are especially susceptible to infection by malaria parasites and other haemosporidians. It is important to understand how immune genes, primarily innate immune genes which are the first line of host defense, have evolved across birds, a highly diverse group of tetrapods. Here, we find that innate immune genes are highly conserved across the avian tree of life and that although most show evidence of positive or diversifying selection within specific lineages or clades, the number of sites is often proportionally low in this broader context of putative constraint. Rather, evidence shows a much higher level of negative or purifying selection in these innate immune genes – rather than adaptive immune genes – which is consistent with birds' long coevolutionary history with pathogens and the need to maintain a rapid response to infection. We further explored avian responses to haemosporidians by comparing differential gene expression in wild birds (1) uninfected with haemosporidians, (2) infected with Plasmodium and (3) infected with Haemoproteus (Parahaemoproteus). We found patterns of significant differential expression with some genes unique to infection with each genus and a few shared between ‘treatment’ groups, but none that overlapped with the genes included in the phylogenetic study.

In this systematic evaluation of fluorescent gel markers (FGM) applied to high-touch surfaces with a metered applicator (MA) made for the purpose versus a generic cotton swab (CS), removal rates were 60.5% (476 of 787) for the MA and 64.3% (506 of 787) for the CS. MA-FGM removal interpretation was more consistent, 83% versus 50% not removed, possibly due to less varied application and more adhesive gel.

A nonlinear Schrödinger equation for the envelope of two-dimensional gravity–capillary waves propagating at the free surface of a vertically sheared current of constant vorticity is derived. In this paper we extend to gravity–capillary wave trains the results of Thomas et al. (Phys. Fluids, 2012, 127102) and complete the stability analysis and stability diagram of Djordjevic & Redekopp (J. Fluid Mech., vol. 79, 1977, pp. 703–714) in the presence of vorticity. The vorticity effect on the modulational instability of weakly nonlinear gravity–capillary wave packets is investigated. It is shown that the vorticity modifies significantly the modulational instability of gravity–capillary wave trains, namely the growth rate and instability bandwidth. It is found that the rate of growth of modulational instability of short gravity waves influenced by surface tension behaves like pure gravity waves: (i) in infinite depth, the growth rate is reduced in the presence of positive vorticity and amplified in the presence of negative vorticity; (ii) in finite depth, it is reduced when the vorticity is positive and amplified and finally reduced when the vorticity is negative. The combined effect of vorticity and surface tension is to increase the rate of growth of modulational instability of short gravity waves influenced by surface tension, namely when the vorticity is negative. The rate of growth of modulational instability of capillary waves is amplified by negative vorticity and attenuated by positive vorticity. Stability diagrams are plotted and it is shown that they are significantly modified by the introduction of the vorticity.