Layering in peralkaline magmas, Ilímaussaq Complex, S Greenland

EJH acknowledges funding from a NERC PhD studentship and the work was completed at the University of St Andrews, UK.The peralkaline to agpaitic Ilímaussaq Complex, S. Greenland, displays spectacular macrorhythmic (> 5 m) layering via the kakortokite (agpaitic nepheline syenite), which outcrops as the lowest exposed rocks in the complex. This study applies crystal size distribution (CSD) analyses and eudialyte-group mineral chemical compositions to study the marker horizon, Unit 0, and the contact to the underlying Unit − 1. Unit 0 is the best-developed unit in the kakortokites and as such is ideal for gaining insight into processes of crystal formation and growth within the layered kakortokite. The findings are consistent with a model whereby the bulk of the black and red layers developed through in situ crystallisation at the crystal mush–magma interface, whereas the white layer developed through a range of processes operating throughout the magma chamber, including density segregation (gravitational settling and flotation). Primary textures were modified through late-stage textural coarsening via grain overgrowth. An open-system model is proposed, where varying concentrations of halogens, in combination with undercooling, controlled crystal nucleation and growth to form Unit 0. Our observations suggest that the model is applicable more widely to the layering throughout the kakortokite series and potentially other layered peralkaline/agpaitic rocks around the world.Publisher PDFPeer reviewe

The role of drug resistance in poor viral suppression in rural South Africa: findings from a population-based study.

BACKGROUND:Understanding factors driving virological failure, including the contribution of HIV drug resistance mutations (DRM), is critical to ensuring HIV treatment remains effective. We examine the contribution of drug resistance mutations for low viral suppression in HIV-positive participants in a population-based sero-prevalence survey in rural South Africa. METHODS:We conducted HIV drug resistance genotyping and ART analyte testing on dried blood spots (DBS) from HIV-positive adults participating in a 2014 survey in North West Province. Among those with virologic failure (> 5000 copies/mL), we describe frequency of DRM to protease inhibitors (PI), nucleoside reverse transcriptase inhibitors (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI), report association of resistance with antiretroviral therapy (ART) status, and assess resistance to first and second line therapy. Analyses are weighted to account for sampling design. RESULTS:Overall 170 DBS samples were assayed for viral load and ART analytes; 78.4% of men and 50.0% of women had evidence of virologic failure and were assessed for drug resistance, with successful sequencing of 76/107 samples. We found ≥1 DRM in 22% of participants; 47% were from samples with detectable analyte (efavirenz, nevirapine or lopinavir). Of those with DRM and detectable analyte, 60% showed high-level resistance and reduced predicted virologic response to ≥1 NRTI/NNRTI typically used in first and second-line regimens. CONCLUSIONS:DRM and predicted reduced susceptibility to first and second-line regimens were common among adults with ART exposure in a rural South African population-based sample. Results underscore the importance of ongoing virologic monitoring, regimen optimization and adherence counseling to optimize durable virologic suppression

HLA Class I Binding Motifs Derived from Random Peptide Libraries Differ at the COOH Terminus from Those of Eluted Peptides

Recombinant HLA-A2, HLA-B8, or HLA-B53 heavy chain produced in Escherichia coli was combined with recombinant β2-microglobulin (β2m) and a pool of randomly synthesised nonamer peptides. This mixture was allowed to refold to form stable major histocompatability complex (MHC) class I complexes, which were then purified by gel filtration chromatography. The peptides bound to the MHC class I molecules were subsequently eluted and sequenced as a pool. Peptide binding motifs for these three MHC class I molecules were derived and compared with previously described motifs derived from analysis of naturally processed peptides eluted from the surface of cells. This comparison indicated that the peptides bound by the recombinant MHC class I molecules showed a similar motif to naturally processed and presented peptides, with the exception of the peptide COOH terminus. Whereas the motifs derived from naturally processed peptides eluted from HLA-A2 and HLA-B8 indicated a strong preference for hydrophobic amino acids at the COOH terminus, this preference was not observed in our studies. We propose that this difference reflects the effects of processing or transport on the peptide repertoire available for binding to MHC class I molecules in vivo

Orbital Torus Imaging: Acceleration, density, and dark matter in the Galactic disk measured with element abundance gradients

Under the assumption of a simple and time-invariant gravitational potential, many Galactic dynamics techniques infer the Milky Way's mass and dark matter distribution from stellar kinematic observations. These methods typically rely on parameterized potential models of the Galaxy and must take into account non-trivial survey selection effects, because they make use of the density of stars in phase space. Large-scale spectroscopic surveys now supply information beyond kinematics in the form of precise stellar label measurements (especially element abundances). These element abundances are known to correlate with orbital actions or other dynamical invariants. Here, we use the Orbital Torus Imaging (OTI) framework that uses abundance gradients in phase space to map orbits. In many cases these gradients can be measured without detailed knowledge of the selection function. We use stellar surface abundances from the APOGEE survey combined with kinematic data from the Gaia mission. Our method reveals the vertical ($z$-direction) orbit structure in the Galaxy and enables empirical measurements of the vertical acceleration field and orbital frequencies in the disk. From these measurements, we infer the total surface mass density, $\Sigma$, and midplane volume density, $\rho_0$, as a function of Galactocentric radius and height. Around the Sun, we find $\Sigma_{\odot}(z=1.1$ kpc)$=72^{+6}_{-9}$M$_{\odot}$pc$^{-2}$ and $\rho_{\odot}(z=0)=0.081^{+0.015}_{-0.009}$ M$_{\odot}$pc$^{-3}$ using the most constraining abundance ratio, [Mg/Fe]. This corresponds to a dark matter contribution in surface density of $\Sigma_{\odot,\mathrm{DM}}(z=1.1$ kpc)$=24\pm4$ M$_{\odot}$pc$^{-2}$, and in total volume mass density of $\rho_{\odot,\mathrm{DM}}(z=0)=0.011\pm0.002$ M$_{\odot}$pc$^{-3}$. Moreover, using these mass density values we estimate the scale length of the low-$\alpha$ disc to be $h_R=2.24\pm0.06$kpc.Comment: Accepted for publication in ApJ. 19 pages, 11 figures, 3 Table

Hysteresis phenomenon in turbulent convection

Coherent large-scale circulations of turbulent thermal convection in air have been studied experimentally in a rectangular box heated from below and cooled from above using Particle Image Velocimetry. The hysteresis phenomenon in turbulent convection was found by varying the temperature difference between the bottom and the top walls of the chamber (the Rayleigh number was changed within the range of $10^7 - 10^8$). The hysteresis loop comprises the one-cell and two-cells flow patterns while the aspect ratio is kept constant ($A=2 - 2.23$). We found that the change of the sign of the degree of the anisotropy of turbulence was accompanied by the change of the flow pattern. The developed theory of coherent structures in turbulent convection (Elperin et al. 2002; 2005) is in agreement with the experimental observations. The observed coherent structures are superimposed on a small-scale turbulent convection. The redistribution of the turbulent heat flux plays a crucial role in the formation of coherent large-scale circulations in turbulent convection.Comment: 10 pages, 9 figures, REVTEX4, Experiments in Fluids, 2006, in pres

Hydrothermal alteration of eudialyte-hosted critical metal deposits : fluid source and implications for deposit grade

MV, AB and AF were funded by the NERC-funded SOS RARE consortium, grant number NE/M010856/1.Eudialyte-hosted critical metal deposits potentially represent major sources of rare earth elements (REE), zirconium and niobium. Here, we study the chemical and isotopic composition of fresh and altered eudialyte in nepheline syenite from the Ilímaussaq Complex, Greenland, one of the world’s largest known eudialyte-hosted deposits. Late-magmatic hydrothermal alteration caused partial replacement of primary magmatic eudialyte by complex pseudomorph assemblages of secondary Zr-, Nb-, and REE-minerals. Three secondary assemblage types are characterised by the zirconosilicates catapleiite, gittinsite and zircon, respectively, of which the catapleiite type is most common. To investigate elemental exchange associated with alteration and to constrain the nature of the metasomatic fluids, we compare trace elements and Sm/Nd isotope compositions of unaltered eudialyte crystals and their replaced counterparts from five syenite samples (three catapleiite-type, one gittinsite-type, and one zircon-type assemblage). Trace element budgets for the catapleiite-type pseudomorphs indicate a 15–30% loss of REE, Ta, Nb, Zr, Sr and Y relative to fresh eudialyte. Moreover, the gittinsite- and zircon-type assemblages record preferential heavy REE (HREE) depletion (≤50%), suggesting that the metasomatic fluids mobilised high field strength elements. Initial Nd isotope ratios of unaltered eudialyte and catapleiite- and gittinsite-type pseudomorphs are indistinguishable, confirming a magmatic fluid origin. However, a higher initial ratio and stronger HREE depletion in the zircon-type pseudomorphs suggests a different source for the zircon-forming fluid. Although alteration reduces the metal budget of the original eudialyte volume, we infer that these elements re-precipitate nearby in the same rock. Alteration, therefore, might have little effect on overall grade but preferentially separates heavy and light REE into different phases. Targeted processing of the alteration products may access individual rare earth families (heavy vs. light) and other metals (Zr, Nb, Ta) more effectively than processing the fresh rock.Publisher PDFPeer reviewe

Hemiretinal vein occlusion 12-month outcomes are unique with vascular endothelial growth factor inhibitors: data from the Fight Retinal Blindness! Registry

BACKGROUND/AIMS To describe baseline characteristics and 12-month outcomes with vascular endothelial growth factor (VEGF) inhibitors of treatment-naïve hemiretinal vein occlusion (HRVO) compared with branch (BRVO) and central (CRVO) variants in routine clinical care. METHODS A database observational study recruited 79 HRVO eyes, 590 BRVO eyes and 344 CRVO eyes that initiated therapy over 10 years. The primary outcome was mean change in visual acuity (VA-letters read on a logarithm of minimal angle of resolution chart) at 12 months. Secondary outcomes included mean change in central subfield thickness (CST), injections and visits. RESULTS At baseline, mean VA in HRVO (53.8) was similar to CRVO (51.9; p=0.40) but lower than BRVO (59.4; p=0.009). HRVO eyes improved to match BRVO eyes from soon after treatment started through 12 months. Mean change in VA was greater in HRVO (+16.4) than both BRVO (+11.4; p=0.006) and CRVO (+8.5; p<0.001). Mean change in CST in HRVO (-231 µm) was similar to CRVO (-259 µm; p=0.33) but greater than BRVO eyes (-151 µm; p=0.003). The groups had similar median burdens of eight injections and nine visits. CONCLUSIONS HRVO generally experienced the greatest mean change in VA of the three types of RVO when treated with VEGF inhibitors, ending with similar 12-month VA and CST to BRVO despite starting closer to CRVO. Inclusion of HRVO in BRVO or CRVO cohorts of clinical trials would be expected to proportionally inflate and skew the visual and anatomic outcomes

Hepatitis C reinfection following treatment induced viral clearance among people who have injected drugs

Background: Although people who inject drugs (PWID) are an important group to receive Hepatitis C Virus (HCV) antiviral therapy, initiation onto treatment remains low. Concerns over reinfection may make clinicians reluctant to treat this group. We examined the risk of HCV reinfection among a cohort of PWID (encompassing all those reporting a history of injecting drug use) from Scotland who achieved a sustained virological response (SVR). Methods: Clinical and laboratory data were used to monitor RNA testing among PWID who attained SVR following therapy between 2000 and 2009. Data were linked to morbidity and mortality records. Follow-up began one year after completion of therapy, ending on 31st December, 2012. Frequency of RNA testing during follow-up was calculated and the incidence of HCV reinfection estimated. Cox proportional hazards regression was used to examine factors associated with HCV reinfection. Results: Among 448 PWID with a SVR, 277 (61.8%) were tested during follow-up, median 4.5 years; 191 (69%) received one RNA test and 86 (31%) received at least two RNA tests. There were seven reinfections over 410 person years generating a reinfection rate of 1.7/100 py (95% CI 0.7–3.5). For PWID who have been hospitalised for an opiate or injection related cause post SVR (11%), the risk of HCV reinfection was greater [AHR = 12.9, 95% CI 2.2–76.0, p = 0.002] and the reinfection rate was 5.7/100 py (95% CI 1.8–13.3). Conclusion: PWID who have been tested, following SVR, for HCV in Scotland appear to be at a low risk of reinfection. Follow-up and monitoring of this population are warranted as treatment is offered more widely