Budgets of turbulent kinetic energy (TKE) and turbulent potential energy (TPE) at different scales $\ell$ in sheared, stably stratified turbulence are analysed using a filtering approach. Competing effects in the flow are considered, along with the physical mechanisms governing the energy fluxes between scales, and the budgets are used to analyse data from direct numerical simulation at buoyancy Reynolds number $Re_b=O(100)$. The mean TKE exceeds the TPE by an order of magnitude at the large scales, with the difference reducing as $\ell$ is decreased. At larger scales, buoyancy is never observed to be positive, with buoyancy always converting TKE to TPE. As $\ell$ is decreased, the probability of locally convecting regions increases, though it remains small at scales down to the Ozmidov scale. The TKE and TPE fluxes between scales are both downscale on average, and their instantaneous values are correlated positively, but not strongly so, and this occurs due to the different physical mechanisms that govern these fluxes. Moreover, the contributions to these fluxes arising from the sub-grid fields are shown to be significant, in addition to the filtered scale contributions associated with the processes of strain self-amplification, vortex stretching and density gradient amplification. Probability density functions (PDFs) of the $Q,R$ invariants of the filtered velocity gradient are considered and show that as $\ell$ increases, the sheared-drop shape of the PDF becomes less pronounced and the PDF becomes more symmetric about $R=0$.

The two-dimensional acoustic wave equation for inviscid compressible boundary layer flows, i.e. the Pridmore-Brown equation with an exponential velocity profile for homentropic flows, is studied for the reflection and over-reflection of acoustic waves based on the exact solution in terms of the confluent Heun function. The reflection coefficient $R$, which is the ratio of the amplitude of the reflected to that of the incoming acoustic wave, is determined as a function of the streamwise wavenumber $\alpha$, the Mach number $M$ and the incident angle $\phi$ of the acoustic waves. Over-reflection refers to $R>1$, i.e. the reflected wave has a larger amplitude than the incident wave. We prove that, in the supersonic context, energy is always transferred from the base flow to the reflected wave, i.e. $R<1$ does not exist. Meanwhile, this fact is intimately linked to the critical layer. We show that the presence of the critical layer leads to an optimal energy exchange from the base flow into the acoustic wave, i.e. the critical layer ensures $R>1$. In our analysis, we observe a special phenomenon, resonant over-reflection, which is proven to be closely related to resonant frequencies $\omega _r$ of unstable modes of the temporal stability of the base flow. At resonant frequencies of the first unstable mode, the over-reflection coefficient exhibits an unusual peak in an extremely narrow frequency interval. The maximum values of these peaks are largely synchronized with the variation of the growth rate $\omega _i$ of the unstable modes. In addition, resonant over-reflection appears also at resonant frequencies of other higher unstable modes, but their peaks of the over-reflection coefficient are always smaller than that induced by the first unstable mode.

Increasing interest in three-dimensional nanostructures adds impetus to electron microscopy techniques capable of imaging at or below the nanoscale in three dimensions. We present a reconstruction algorithm that takes as input a focal series of four-dimensional scanning transmission electron microscopy (4D-STEM) data. We apply the approach to a lead iridate, Pb$_2$Ir$_2$O$_7$, and yttrium-stabilized zirconia, Y$_{0.095}$Zr$_{0.905}$O$_2$, heterostructure from data acquired with the specimen in a single plan-view orientation, with the epitaxial layers stacked along the beam direction. We demonstrate that Pb–Ir atomic columns are visible in the uppermost layers of the reconstructed volume. We compare this approach to the alternative techniques of depth sectioning using differential phase contrast scanning transmission electron microscopy (DPC-STEM) and multislice ptychographic reconstruction.

The enzyme 5,10-methylenetetrahydrofolate reductase (MTHFR) links the folate cycle that produces one-carbon units with the methionine cycle that converts these into S-adenosylmethionine (SAM), the universal methyl donor for almost all methyltransferases. Previously, MTHFR has been shown to be regulated by phosphorylation, which suppresses its activity. SAM levels have been shown to increase substantially soon after initiation of meiotic maturation of the mouse germinal vesicle (GV) stage oocyte and then decrease back to their original low level in mature second meiotic metaphase (MII) eggs. As MTHFR controls the entry of one-carbon units into the methionine cycle, it is a candidate regulator of the SAM levels in oocytes and eggs. Mthfr transcripts are expressed in mouse oocytes and preimplantation embryos and MTHFR protein is present at each stage. In mature MII eggs, the apparent molecular weight of MTHFR was increased compared with GV oocytes, which we hypothesized was due to increased phosphorylation. The increase in apparent molecular weight was reversed by treatment with lambda protein phosphatase (LPP), indicating that MTHFR is phosphorylated in MII eggs. In contrast, LPP had no effect on MTHFR from GV oocytes, 2-cell embryos, or blastocysts. MTHFR was progressively phosphorylated after initiation of meiotic maturation, reaching maximal levels in MII eggs before decreasing again after egg activation. As phosphorylation suppresses MTHFR activity, it is predicted that MTHFR becomes inactive during meiotic maturation and is minimally active in MII eggs, which is consistent with the reported changes in SAM levels during mouse oocyte maturation.

Background: Proteogenomics, the integration of proteomics and RNASeq expands the discovery landscape for candidate expressed gene networks to obtain novel insights into host response in post-infectious hydrocephalus (PIH). We examined the cerebrospinal fluid (CSF) of infants with PIH, and case controlled against age-matched infants with non-postinfectious hydrocephalus (NPIH) to probe the molecular mechanisms of PIH, leveraging molecular identification of bacterial and viral pathogens. Methods: Ventricular CSF samples of 100 infants ≤ 3 months of age with PIH (n=64) and NPIH (n=36) were analyzed with proteomics and RNASeq. 16S rRNA/DNA sequencing and virome capture identified Paenibacillus spp. and cytomegalovirus as dominant pathogenetic bacteria implicated in our PIH cohort. Proteogenomics assessed differential expression, gene set enrichment and activated gene pathways. Results: Of 616 proteins and 11,114 genes, there was enrichment for the immune system, cell-cell junction signaling and response to oxidative stress. Proteogenomics yielded 33 functionally and genetically associated gene sets related to neutrophil activation, platelet activation, and cytokines (interleukins and interferon) signaling. Conclusions: We identified PIH patients with severe disease at time of hydrocephalus surgery, to have differential expression of proteins/genes involved in neuroinflammation, ependymal barrier integrity and reaction to oxidative stress. Further studies are needed to examine those proteins/genes as biomarkers for PIH.

Ediacaran cap dolostone atop Marinoan glacial deposits contains complex sedimentary structures with extremely negative δ13Ccarb values in close association with oscillations in palaeoclimatic and oceanographic proxy records. However, the precise geological, geochronological and geochemical context of the cap dolostone is not clarified, which hampers us from correctly interpreting the extremely negative δ13Ccarb values and their causal relationships with the Snowball Earth hypothesis. In this study, we conducted detailed in situ geochronological and geochemical analyses on the calcite within the cap dolostone from the Ediacaran Doushantuo Formation in South China in order to define its formation and relationship to the Snowball Earth hypothesis. Petrographic observations show that formation of dolomite pre-dates precipitation of calcite and pyrite, which pre-dates quartz cementation in the basal cap carbonate. Calcite cement within the cap dolostone yielded a U–Pb age of 636.5 ± 7.4/17.8 Ma (2σ, MSWD = 1.6, n = 36/40), which is within uncertainty of a published dolomite U–Pb age of 632 ± 17 Ma (recalculated as 629.3 ± 16.7/22.9 Ma). These age constraints negate the possibility that the calcite cement was formed by late Ediacaran or Cambrian hydrothermal activity. The rare earth element distribution patterns suggest a dominant seawater origin overprinted by subsequent early Ediacaran hydrothermal activity. The combined age, petrographic and geochemical data suggest oxidization of methane clathrates in response to complicated interplay between eustasy and isostatic rebound and hydrothermal fluids.

Magnetohydrodynamic (MHD) simulations of the solar corona have become more popular with the increased availability of computational power. Modern computational plasma codes, relying upon computational fluid dynamics (CFD) methods, allow the coronal features to be resolved using solar surface magnetograms as inputs. These computations are carried out in a full three-dimensional domain and, thus, selection of the correct mesh configuration is essential to save computational resources and enable/speed up convergence. In addition, it has been observed that for MHD simulations close to the hydrostatic equilibrium, spurious numerical artefacts might appear in the solution following the mesh structure, which makes the selection of the grid also a concern for accuracy. The purpose of this paper is to discuss and trade off two main mesh topologies when applied to global solar corona simulations using the unstructured ideal MHD solver from the COOLFluiD platform. The first topology is based on the geodesic polyhedron and the second on $UV$ mapping. Focus is placed on aspects such as mesh adaptability, resolution distribution, resulting spurious numerical fluxes and convergence performance. For this purpose, first a rotating dipole case is investigated, followed by two simulations using real magnetograms from the solar minima (1995) and solar maxima (1999). It is concluded that the most appropriate mesh topology for the simulation depends on several factors, such as the accuracy requirements, the presence of features near the polar regions and/or strong features in the flow field in general. If convergence is of concern and the simulation contains strong dynamics, then grids which are based on the geodesic polyhedron are recommended compared with more conventionally used $UV$-mapped meshes.

We performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) antinucleocapsid IgG testing on 5,557 healthcare providers and found a seroprevalence of 3.9%. African Americans were more likely to test positive than Whites, and HCWs with household exposure and those working on COVID-19 cohorting units were more likely to test positive than their peers.

This paper proposes an online entry trajectory planning based on predictor corrector algorithm that satisfies terminal constraints, path constraints and geographic constraints for lifting-body entry vehicles. The vehicle is considered as a 3DOF point mass. A piecewise linear bank profile in the altitude-versus-velocity (H-V) plane is used to project the longitudinal trajectory and a heading angle corridor-based bank angle reversal logic is designed to satisfy the geographic constraints simultaneously. The algorithm in longitudinal plane solves the problem of the mismatch between terminal range and height and the algorithm in lateral plane satisfies the no-fly zone constraint. Simulation results with the CAV-H model show that the proposed algorithm can generate entry trajectories satisfying multiple constraints and has certain robustness.

Cutaneous leishmaniasis (CL) is a spectrum of clinical manifestations characterized by severe skin ulcerations that leads to social stigma. There are limited treatment options for CL, and the available drugs are becoming less efficacious due to drug resistance. More efficacious and safer antileishmanial drugs are needed. In this study, the biological effect of seven synthetically accessible nitroaromatic compounds was evaluated in vitro against amastigotes of Leishmania amazonensis, followed by in vivo evaluation using mouse models of CL. Two compounds (6 and 7) were active against amastigotes in vitro [half-maximal effective concentration (EC50): 4.57 ± 0.08 and 9.19 ± 0.68 μm, respectively], with selectivity indexes >50, and the other compounds were not selective. In vivo, compounds 6 and 7 (10 mg kg−1, twice a day for 14 days) failed to reduce skin lesion sizes and parasite loads determined by light microscopy of lesion imprints and quantitative polymerase chain reaction. Nevertheless, the in vitro leishmanicidal efficacy sustained their use as templates for nitroimidazole-based antileishmanial drug discovery programmes focusing on analogues with more suitable properties.

To persist (without immigration) in habitats with unpredictable environmental conditions, annuals must produce seeds each year or have a seed bank. Thus, we predicted that compared to perennials, annuals have a wider germination temperature range (GTR, the difference in temperature between the week with the highest and the week with the lowest germination during the natural germination season). We determined the GTR via germination phenology data for 350 herbaceous species in 59 families from the eastern USA: summer annuals (SA), 63; winter annuals (WA), 83; monocarpic perennials (MP), 28; and polycarpic perennials (PP), 176. There was no significant phylogenetic signal for the GTR. The width of the GTR during the first spring germination season was 9.6, 8.7 and 8.8°C for MP, PP and SA, respectively, and during the first autumn germination season 12.8, 11.8 and 12.4°C for MP, PP and WA, respectively. Annuals did not have a wider GTR than perennials in either the spring or the autumn germination season. Our data suggest that selection for early germination in either spring or autumn has resulted in only small differences in the GTR. We predict that global warming will have little or no effect on reshaping the germination phenology of herbaceous species of temperate eastern North America.