Spatial variability in shrub vegetation across dune forms in central Saudi Arabia

In desert dune environments, vegetation may be an indicator of dune stability and rates of sediment transport. As topography and underlying controls of vegetation vary over large spatial areas variations in dune form make scaling up of field research difficult. To mitigate this, and to identify spatial variations in vegetation distributions in a Saudi Arabian sand sea, spectral information from high resolution satellite images was classified to map polygons of shrub vegetation over 360 km2 of well-defined linear dunes, broken linear dunes and dome dune forms. When compared to topographic characteristics of the landscape extracted from a digital elevation model, vegetation densities were often highest on 10 to 20-degree slopes elevated above interdune salt deposits on dune flanks. Spatially this was confined to small areas, and density was not always related to dune form, more to the presence of groundwater which could also encourage vegetation on the tops of some dunes. Field observations identified shrubs of mainly Calligonum genus whose size is related to the amounts of salts, moving sediment and access to the water table that varies within and between dune forms. Shrub vegetation density is likened to surface roughness to better understand sediment movement in this environment

Late-Time Spectral Observations of the Strongly Interacting Type Ia Supernova PTF11kx

PTF11kx was a Type Ia supernova (SN Ia) that showed time-variable absorption features, including saturated Ca II H&K lines that weakened and eventually went into emission. The strength of the emission component of H{\alpha} increased, implying that the SN was undergoing significant interaction with its circumstellar medium (CSM). These features were blueshifted slightly and showed a P-Cygni profile, likely indicating that the CSM was directly related to, and probably previously ejected by, the progenitor system itself. These and other observations led Dilday et al. (2012) to conclude that PTF11kx came from a symbiotic nova progenitor like RS Oph. In this work we extend the spectral coverage of PTF11kx to 124-680 rest-frame days past maximum brightness. These spectra of PTF11kx are dominated by H{\alpha} emission (with widths of ~2000 km/s), strong Ca II emission features (~10,000 km/s wide), and a blue "quasi-continuum" due to many overlapping narrow lines of Fe II. Emission from oxygen, He I, and Balmer lines higher than H{\alpha} is weak or completely absent at all epochs, leading to large observed H{\alpha}/H{\beta} intensity ratios. The broader (~2000 km/s) H{\alpha} emission appears to increase in strength with time for ~1 yr, but it subsequently decreases significantly along with the Ca II emission. Our latest spectrum also indicates the possibility of newly formed dust in the system as evidenced by a slight decrease in the red wing of H{\alpha}. During the same epochs, multiple narrow emission features from the CSM temporally vary in strength. The weakening of the H{\alpha} and Ca II emission at late times is possible evidence that the SN ejecta have overtaken the majority of the CSM and agrees with models of other strongly interacting SNe Ia. The varying narrow emission features, on the other hand, may indicate that the CSM is clumpy or consists of multiple thin shells.Comment: 12 pages, 7 figures, 1 table, re-submitted to Ap

Inequity in access to transplantation in the UK

Background and objectives Despite the presence of a universal health care system, it is unclear if there is intercenter variation in access to kidney transplantation in the United Kingdom. This study aims to assess whether equity exists in access to kidney transplantation in the United Kingdom after adjustment for patient-specific factors and center practice patterns. Design, setting, participants, & measurements In this prospective, observational cohort study including all 71 United Kingdom kidney centers, incident RRT patients recruited between November 2011 and March 2013 as part of the Access to Transplantation and Transplant Outcome Measures study were analyzed to assess preemptive listing (n=2676) and listing within 2 years of starting dialysis (n=1970) by center. Results Seven hundred and six participants (26%) were listed preemptively, whereas 585 (30%) were listed within 2 years of commencing dialysis. The interquartile range across centers was 6%–33% for preemptive listing and 25%–40% for listing after starting dialysis. Patient factors, including increasing age, most comorbidities, body mass index >35 kg/m2, and lower socioeconomic status, were associated with a lower likelihood of being listed and accounted for 89% and 97% of measured intercenter variation for preemptive listing and listing within 2 years of starting dialysis, respectively. Asian (odds ratio, 0.49; 95% confidence interval, 0.33 to 0.72) and Black (odds ratio, 0.43; 95% confidence interval, 0.26 to 0.71) participants were both associated with reduced access to preemptive listing; however Asian participants were associated with a higher likelihood of being listed after starting dialysis (odds ratio, 1.42; 95% confidence interval, 1.12 to 1.79). As for center factors, being registered at a transplanting center (odds ratio, 3.1; 95% confidence interval, 2.36 to 4.07) and a universal approach to discussing transplantation (odds ratio, 1.4; 95% confidence interval, 1.08 to 1.78) were associated with higher preemptive listing, whereas using a written protocol was associated negatively with listing within 2 years of starting dialysis (odds ratio, 0.7; 95% confidence interval, 0.58 to 0.9). Conclusions Patient case mix accounts for most of the intercenter variation seen in access to transplantation in the United Kingdom, with practice patterns also contributing some variation. Socioeconomic inequity exists despite having a universal health care system

Seminal plasma and prostaglandin E2 up-regulate fibroblast growth factor 2 expression in endometrial adenocarcinoma cells via E-series prostanoid-2 receptor-mediated transactivation of the epidermal growth factor receptor and extracellular signal-regulated kinase pathway

We report a multiwavelength (X-ray, ultraviolet/optical/infrared, radio) analysis of the relativistic tidal disruption event candidate Sw J2058+05 from 3 months to 3 yr post-discovery in order to study its properties and compare its behavior with that of Sw J1644+57. Our main results are as follows. (1) The long-term X-ray light curve of Sw J2058+05 shows a remarkably similar trend to that of Sw J1644+57. After a prolonged power-law decay, the X-ray flux drops off rapidly by a factor of $\gtrsim 160$ within a span of $\Delta$$t$/$t$ $\le$ 0.95. Associating this sudden decline with the transition from super-Eddington to sub-Eddington accretion, we estimate the black hole mass to be in the range of $10^{4-6}$ M$_{\odot}$. (2) We detect rapid ($\lesssim 500$ s) X-ray variability before the dropoff, suggesting that, even at late times, the X-rays originate from close to the black hole (ruling out a forward-shock origin). (3) We confirm using HST and VLBA astrometry that the location of the source coincides with the galaxy's center to within $\lesssim 400$ pc (in projection). (4) We modeled Sw J2058+05's ultraviolet/optical/infrared spectral energy distribution with a single-temperature blackbody and find that while the radius remains more or less constant at a value of $63.4 \pm 4.5$ AU ($\sim 10^{15}$ cm) at all times during the outburst, the blackbody temperature drops significantly from $\sim$ 30,000 K at early times to a value of $\sim$ 15,000 K at late times (before the X-ray dropoff). Our results strengthen Sw J2058+05's interpretation as a tidal disruption event similar to Sw J1644+57.Comment: Replaced with the published version of the manuscrip

Identification of typical ecohydrological behaviours using InSAR allows landscape-scale mapping of peatland condition

Better tools for rapid and reliable assessment of global peatland extent and condition are urgently needed to support action to prevent further decline of peatlands. Peatland surface motion is a response to changes in the water and gas content of a peat body regulated by the ecology and hydrology of a peatland system. Surface motion is therefore a sensitive measure of ecohydrological condition but has traditionally been impossible to measure at the landscape scale. Here we examine the potential of surface motion metrics derived from satellite interferometric synthetic aperture radar (InSAR) to map peatland condition in a blanket bog landscape. We show that the timing of maximum seasonal swelling of the peat is characterised by a bimodal distribution. The first maximum, usually in autumn, is typical of "stiffer"peat associated with steeper topographic gradients, peatland margins, and degraded peatland and more often associated with "shrub"-dominated vegetation communities. The second maximum, usually in winter, is typically associated with "softer"peat typically found in low topographic gradients often featuring pool systems and Sphagnum-dominated vegetation communities. Specific conditions of "soft"and "stiff"peats are also determined by the amplitude of swelling and multi-annual average motion. Peatland restoration currently follows a re-wetting strategy; however, our approach highlights that landscape setting appears to determine the optimal endpoint for restoration. Aligning the expectation for restoration outcomes with landscape setting might optimise peatland stability and carbon storage. Importantly, deployment of this approach, based on surface motion dynamics, could support peatland mapping and management on a global scale

XRate: a fast prototyping, training and annotation tool for phylo-grammars

BACKGROUND: Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists. RESULTS: We have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures. CONCLUSION: Our results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools

Synthesis and characterization of dual-functionalized core-shell fluorescent microspheres for bioconjugation and cellular delivery

The efficient transport of micron-sized beads into cells, via a non-endocytosis mediated mechanism, has only recently been described. As such there is considerable scope for optimization and exploitation of this procedure to enable imaging and sensing applications to be realized. Herein, we report the design, synthesis and characterization of fluorescent microsphere-based cellular delivery agents that can also carry biological cargoes. These core-shell polymer microspheres possess two distinct chemical environments; the core is hydrophobic and can be labeled with fluorescent dye, to permit visual tracking of the microsphere during and after cellular delivery, whilst the outer shell renders the external surfaces of the microspheres hydrophilic, thus facilitating both bioconjugation and cellular compatibility. Cross-linked core particles were prepared in a dispersion polymerization reaction employing styrene, divinylbenzene and a thiol-functionalized co-monomer. These core particles were then shelled in a seeded emulsion polymerization reaction, employing styrene, divinylbenzene and methacrylic acid, to generate orthogonally functionalized core-shell microspheres which were internally labeled via the core thiol moieties through reaction with a thiol reactive dye (DY630-maleimide). Following internal labeling, bioconjugation of green fluorescent protein (GFP) to their carboxyl-functionalized surfaces was successfully accomplished using standard coupling protocols. The resultant dual-labeled microspheres were visualized by both of the fully resolvable fluorescence emissions of their cores (DY630) and shells (GFP). In vitro cellular uptake of these microspheres by HeLa cells was demonstrated conventionally by fluorescence-based flow cytometry, whilst MTT assays demonstrated that 92% of HeLa cells remained viable after uptake. Due to their size and surface functionalities, these far-red-labeled microspheres are ideal candidates for in vitro, cellular delivery of proteins, as described in the accompanying paper

Signal peptide peptidase (SPP) dimer formation as assessed by fluorescence lifetime imaging microscopy (FLIM) in intact cells

BACKGROUND: Signal peptide peptidase (SPP) is an intramembrane cleaving protease identified by its cleavage of several type II membrane signal peptides. Conservation of intramembrane active site residues demonstrates that SPP, SPP family members, and presenilins (PSs) make up a family of intramembrane cleaving proteases. Because SPP appears to function without additional protein cofactors, the study of SPP may provide structural insights into the mechanism of intramembrane proteolysis by this biomedically important family of proteins. Previous studies have shown that SPP isolated from cells appears to be a homodimer, but some evidence exists that in vitro SPP may be active as a monomer. We have conducted additional experiments to determine if SPP exists as a monomer or dimer in vivo. RESULTS: Fluorescence lifetime imaging microscopy (FLIM) can be is used to determine intra- or intermolecular interactions by fluorescently labeling epitopes on one or two different molecules. If the donor and acceptor fluorophores are less than 10 nm apart, the donor fluorophore lifetime shortens proportionally to the distance between the fluorophores. In this study, we used two types of fluorescence energy transfer (FRET) pairs; cyan fluorescent protein (CFP) with yellow fluorescent protein (YFP) or Alexa 488 with Cy3 to differentially label the NH2- or COOH-termini of SPP molecules. A cell based SPP activity assay was used to show that all tagged SPP proteins are proteolytically active. Using FLIM we were able to show that the donor fluorophore lifetime of the CFP tagged SPP construct in living cells significantly decreases when either a NH2- or COOH-terminally YFP tagged SPP construct is co-transfected, indicating close proximity between two different SPP molecules. These data were then confirmed in cell lines stably co-expressing V5- and FLAG-tagged SPP constructs. CONCLUSION: Our FLIM data strongly suggest dimer formation between two separate SPP proteins. Although the tagged SPP constructs are expressed throughout the cell, SPP dimer detection by FLIM is seen predominantly at or near the plasma membrane

Exploring the Optical Transient Sky with the Palomar Transient Factory

The Palomar Transient Factory (PTF) is a wide-field experiment designed to investigate the optical transient and variable sky on time scales from minutes to years. PTF uses the CFH12k mosaic camera, with a field of view of 7.9 deg^2 and a plate scale of 1 asec/pixel, mounted on the the Palomar Observatory 48-inch Samuel Oschin Telescope. The PTF operation strategy is devised to probe the existing gaps in the transient phase space and to search for theoretically predicted, but not yet detected, phenomena, such as fallback supernovae, macronovae, .Ia supernovae and the orphan afterglows of gamma-ray bursts. PTF will also discover many new members of known source classes, from cataclysmic variables in their various avatars to supernovae and active galactic nuclei, and will provide important insights into understanding galactic dynamics (through RR Lyrae stars) and the Solar system (asteroids and near-Earth objects). The lessons that can be learned from PTF will be essential for the preparation of future large synoptic sky surveys like the Large Synoptic Survey Telescope. In this paper we present the scientific motivation for PTF and describe in detail the goals and expectations for this experiment.Comment: 15 pages, 6 figures, submitted to PAS

Swift J2058.4+0516: Discovery of a Possible Second Relativistic Tidal Disruption Flare?

We report the discovery by the Swift hard X-ray monitor of the transient source Swift J2058.4+0516 (Sw J2058+05). Our multi-wavelength follow-up campaign uncovered a long-lived (duration >~ months), luminous X-ray (L_X,iso ~ 3 x 10^47 erg s^-1) and radio (nu L_nu,iso ~ 10^42 erg s^-1) counterpart. The associated optical emission, however, from which we measure a redshift of 1.1853, is relatively faint, and this is not due to a large amount of dust extinction in the host galaxy. Based on numerous similarities with the recently discovered GRB 110328A / Swift J164449.3+573451 (Sw J1644+57), we suggest that Sw J2058+05 may be the second member of a new class of relativistic outbursts resulting from the tidal disruption of a star by a supermassive black hole. If so, the relative rarity of these sources (compared with the expected rate of tidal disruptions) implies that either these outflows are extremely narrowly collimated (theta < 1 degree), or only a small fraction of tidal disruptions generate relativistic ejecta. Analogous to the case of long-duration gamma-ray bursts and core-collapse supernovae, we speculate that rapid spin of the black hole may be a necessary condition to generate the relativistic component. Alternatively, if powered by gas accretion (i.e., an active galactic nucleus [AGN]), Sw J2058+05 would seem to represent a new mode of variability in these sources, as the observed properties appear largely inconsistent with known classes of AGNs capable of generating relativistic jets (blazars, narrow-line Seyfert 1 galaxies).Comment: Minor typos correcte