A kinetic Monte-Carlo methodology is presented for simulating crystal growth in materials which contain stacking faults. By simulating a large number of potential growth and dissolution events, a ...representation of the crystal is generated at various stages throughout the crystallisation, allowing the effects of disorder on the evolution of crystal habit and nanoscale surface topography to be explored. As examples, simulations were performed on two intergrown zeolite materials - zeolite T and zeolite beta. In both zeolite T and zeolite beta, simulations demonstrate how an intergrown structure leads to a characteristic roughening of certain crystal facets. In zeolite beta, this is accompanied by the development of internal defects which shows a non-homogeneous distribution. Results of simulations are validated by direct comparison to experimental scanning electron microscopy, atomic force microscopy and X-ray diffraction data. All simulations are performed using the CrystalGrower software package with modifications to account for disorder and should be generally applicable to all classes of crystals.
A kinetic Monte Carlo approach for modelling crystal growth, allowing simulation of crystal habit and surface fine structure in materials containing high levels of stacking faults.
Diffusion magnetic resonance imaging (dMRI) is widely used to probe tissue microstructure, and is currently the only non-invasive way to measure the brain's fiber architecture. While a large number ...of approaches to recover the intra-voxel fiber structure have been utilized in the scientific community, a direct, 3D, quantitative validation of these methods against relevant histological fiber geometries is lacking. In this study, we investigate how well different high angular resolution diffusion imaging (HARDI) models and reconstruction methods predict the ground-truth histologically defined fiber orientation distribution (FOD), as well as investigate their behavior over a range of physical and experimental conditions. The dMRI methods tested include constrained spherical deconvolution (CSD), Q-ball imaging (QBI), diffusion orientation transform (DOT), persistent angular structure (PAS), and neurite orientation dispersion and density imaging (NODDI) methods. Evaluation criteria focus on overall agreement in FOD shape, correct assessment of the number of fiber populations, and angular accuracy in orientation. In addition, we make comparisons of the histological orientation dispersion with the fiber spread determined from the dMRI methods. As a general result, no HARDI method outperformed others in all quality criteria, with many showing tradeoffs in reconstruction accuracy. All reconstruction techniques describe the overall continuous angular structure of the histological FOD quite well, with good to moderate correlation (median angular correlation coefficient > 0.70) in both single- and multiple-fiber voxels. However, no method is consistently successful at extracting discrete measures of the number and orientations of FOD peaks. The major inaccuracies of all techniques tend to be in extracting local maxima of the FOD, resulting in either false positive or false negative peaks. Median angular errors are ∼10° for the primary fiber direction and ∼20° for the secondary fiber, if present. For most methods, these results did not vary strongly over a wide range of acquisition parameters (number of diffusion weighting directions and b value). Regardless of acquisition parameters, all methods show improved successes at resolving multiple fiber compartments in a voxel when fiber populations cross at near-orthogonal angles, with no method adequately capturing low to moderate angle (<60°) crossing fibers. Finally, most methods are limited in their ability to capture orientation dispersion, resulting in low to moderate, yet statistically significant, correlation with histologically-derived dispersion with both HARDI and NODDI methodologies. Together, these results provide quantitative measures of the reliability and limitations of dMRI reconstruction methods and can be used to identify relative advantages of competing approaches as well as potential strategies for improving accuracy.
•3D histological validation of diffusion MRI measures of fiber orientation.•All methods capture the overall structure of the FOD quite well.•Most inaccuracies occur when extracting discrete peaks from the FOD.•No method consistently resolves fibers crossing at low to moderate angles.•Measures of dispersion show modest correlation with histological measures.
Large-eddy simulation was used to model turbulent atmospheric surface layer (ASL) flow over canopies composed of streamwise-aligned rows of synthetic trees of height, $h$, and systematically arranged ...to quantify the response to variable streamwise spacing, $\delta _1$, and spanwise spacing, $\delta _2$, between adjacent trees. The response to spanwise and streamwise heterogeneity has, indeed, been the topic of a sustained research effort: the former resulting in formation of Reynolds-averaged counter-rotating secondary cells, the latter associated with the $k$- and $d$-type response. No study has addressed the confluence of both, and results herein show secondary flow polarity reversal across ‘critical’ values of $\delta _1$ and $\delta _2$. For $\delta _2/\delta \lesssim 1$ and $\gtrsim 2$, where $\delta$ is the flow depth, the counter-rotating secondary cells are aligned such that upwelling and downwelling, respectively, occurs above the elements. The streamwise spacing $\delta _1$ regulates this transition, with secondary cell reversal occurring first for the largest $k$-type cases, as elevated turbulence production within the canopy necessitates entrainment of fluid from aloft. The results are interpreted through the lens of a benchmark prognostic closure for effective aerodynamic roughness, $z_{0,{Eff.}} = \alpha \sigma _h$, where $\alpha$ is a proportionality constant and $\sigma _h$ is height root mean square. We report $\alpha \approx 10^{-1}$, the value reported over many decades for a broad range of rough surfaces, for $k$-type cases at small $\delta _2$, whereas the transition to $d$-type arrangements necessitates larger $\delta _2$. Though preliminary, results highlight the non-trivial response to variation of streamwise and spanwise spacing.
Agromining: Farming for Metals in the Future? van der Ent, Antony; Baker, Alan J. M; Reeves, Roger D ...
Environmental science & technology,
04/2015, Letnik:
49, Številka:
8
Journal Article
Recenzirano
Odprti dostop
Phytomining technology employs hyperaccumulator plants to take up metal in harvestable plant biomass. Harvesting, drying and incineration of the biomass generates a high-grade bio-ore. We propose ...that “agromining” (a variant of phytomining) could provide local communities with an alternative type of agriculture on degraded lands; farming not for food crops, but for metals such as nickel (Ni). However, two decades after its inception and numerous successful experiments, commercial phytomining has not yet become a reality. To build the case for the minerals industry, a large-scale demonstration is needed to identify operational risks and provide “real-life” evidence for profitability.
Abstract
Background
Commercially available SARS-CoV-2 serological assays based on different viral antigens have been approved for the qualitative determination of anti-SARS-CoV-2 antibodies. However, ...there are limited published data associating the results from commercial assays with neutralizing antibodies.
Methods
Sixty-six specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys Anti-SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Correlation, concordance, positive percent agreement (PPA), and negative percent agreement (NPA) were calculated at several cutoffs. Results were compared in patients categorized by clinical outcomes.
Results
The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46, respectively. At an EC50 of 1:32, the concordance kappa with Roche was 0.49 (95% CI; 0.23–0.75), with Abbott was 0.52 (0.28–0.77), and with EUROIMMUN was 0.61 (0.4–0.82). At the same neutralizing titer, the PPA and NPA for the Roche was 100% (94–100) and 56% (30–80); Abbott was 96% (88–99) and 69% (44–86); and EUROIMMUN was 91% (80–96) and 81% (57–93) for distinguishing neutralizing antibodies. Patients who were intubated, had cardiac injury, or acute kidney injury from COVID-19 infection had higher neutralizing titers relative to those with mild symptoms.
Conclusions
COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. Nevertheless, commercial serological assays have poor NPA for SARS-CoV-2 neutralization, making them imperfect proxies for neutralization.
Observational and computational studies of inertia-dominated wall turbulence with unstable thermal stratification have demonstrated that the inclination angle of large-scale motions (LSMs) increases ...with increasing buoyancy (as characterized by the Monin–Obukhov stability variable
$\unicodeSTIX{x1D701}_{z}$
). The physical implications of this structural steepening have received relatively less attention. Some authors have proposed that LSMs thicken – yet remain attached to the wall – with increasing buoyancy (Salesky & Anderson,
J. Fluid Mech.
, vol. 856, 2018, pp. 135–168), while others have presented evidence that the upstream edge of an LSM remains anchored to the wall while its downstream edge lifts away from the wall (Hommema & Adrian,
Boundary-Layer Meteorol.
, vol. 106, 2003, pp. 147–170). Using a suite of large-eddy simulations (LES) of unstably stratified turbulent channel flow, we demonstrate that buoyancy acts to lift LSMs away from the wall, leaving a wedge of fluid beneath with differing momentum. We develop a prognostic model for LSM inclination angle that accounts for this observed structure, where the LSM inclination angle
$\unicodeSTIX{x1D6FE}$
is the sum of the inclination angle observed in a neutrally stratified wall-bounded turbulent flow,
$\unicodeSTIX{x1D6FE}_{0}\approx 12^{\circ }{-}15^{\circ }$
, and the stability-dependent inclination angle of the wedge
$\unicodeSTIX{x1D6FE}_{w}(\unicodeSTIX{x1D701}_{z})$
. Reported values of
$\unicodeSTIX{x1D6FE}(\unicodeSTIX{x1D701}_{z})$
from the literature, LES results and atmospheric surface layer observations are found to be in good agreement with the new model for
$\unicodeSTIX{x1D6FE}(\unicodeSTIX{x1D701}_{z})$
.
Accurate estimates of the BOLD hemodynamic response function (HRF) are crucial for the interpretation and analysis of event-related functional MRI data. To date, however, there have been no ...comprehensive measurements of the HRF in white matter (WM) despite increasing evidence that BOLD signals in WM change after a stimulus. We performed an event-related cognitive task (Stroop color-word interference) to measure the HRF in selected human WM pathways. The task was chosen in order to produce robust, distributed centers of activity throughout the cortex. To measure the HRF in WM, fiber tracts were reconstructed between each pair of activated cortical areas. We observed clear task-specific HRFs with reduced magnitudes, delayed onsets and prolonged initial dips in WM tracts compared with activated grey matter, thus calling for significant changes to current standard models for accurately characterizing the HRFs in WM and for modifications of standard methods of analysis of functional imaging data.
Tropical cyclones (TCs) are a hazard to life and property and a prominent element of the global climate system; therefore, understanding and predicting TC location, intensity, and frequency is of ...both societal and scientific significance. Methodologies exist to predict basinwide, seasonally aggregated TC activity months, seasons, and even years in advance. It is shown that a newly developed high-resolution global climate model can produce skillful forecasts of seasonal TC activity on spatial scales finer than basinwide, from months and seasons in advance of the TC season. The climate model used here is targeted at predicting regional climate and the statistics of weather extremes on seasonal to decadal time scales, and comprises high-resolution (50 km × 50 km) atmosphere and land components as well as more moderate-resolution (∼100 km) sea ice and ocean components. The simulation of TC climatology and interannual variations in this climate model is substantially improved by correcting systematic ocean biases through “flux adjustment.” A suite of 12-month duration retrospective forecasts is performed over the 1981–2012 period, after initializing the climate model to observationally constrained conditions at the start of each forecast period, using both the standard and flux-adjusted versions of the model. The standard and flux-adjusted forecasts exhibit equivalent skill at predicting Northern Hemisphere TC season sea surface temperature, but the flux-adjusted model exhibits substantially improved basinwide and regional TC activity forecasts, highlighting the role of systematic biases in limiting the quality of TC forecasts. These results suggest that dynamical forecasts of seasonally aggregated regional TC activity months in advance are feasible.
Celotno besedilo
Dostopno za:
BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Membrane lateral heterogeneity is accepted as a requirement for the function of biological membranes and the notion of lipid rafts gives specificity to this broad concept. However, the lipid raft ...field is now at a technical impasse because the physical tools to study biological membranes as a liquid that is ordered in space and time are still being developed. This has lead to a disconnection between the concept of lipid rafts as derived from biochemical and biophysical assays and their existence in the cell. Here, we compare the concept of lipid rafts as it has emerged from the study of synthetic membranes with the reality of lateral heterogeneity in biological membranes. Further application of existing tools and the development of new tools are needed to understand the dynamic heterogeneity of biological membranes.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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