Automated Morphological Classification of SDSS Red Sequence Galaxies

(abridged) In the last decade, the advent of enormous galaxy surveys has motivated the development of automated morphological classification schemes to deal with large data volumes. Existing automated schemes can successfully distinguish between early and late type galaxies and identify merger candidates, but are inadequate for studying detailed morphologies of red sequence galaxies. To fill this need, we present a new automated classification scheme that focuses on making finer distinctions between early types roughly corresponding to Hubble types E, S0, and Sa. We visually classify a sample of 984 non-starforming SDSS galaxies with apparent sizes >14". We then develop an automated method to closely reproduce the visual classifications, which both provides a check on the visual results and makes it possible to extend morphological analysis to much larger samples. We visually classify the galaxies into three bulge classes (BC) by the shape of the light profile in the outer regions: discs have sharp edges and bulges do not, while some galaxies are intermediate. We separately identify galaxies with features: spiral arms, bars, clumps, rings, and dust. We find general agreement between BC and the bulge fraction B/T measured by the galaxy modeling package GIM2D, but many visual discs have B/T>0.5. Three additional automated parameters -- smoothness, axis ratio, and concentration -- can identify many of these high-B/T discs to yield automated classifications that agree ~70% with the visual classifications (>90% within one BC). Both methods are used to study the bulge vs. disc frequency as a function of four measures of galaxy 'size': luminosity, stellar mass, velocity dispersion, and radius. All size indicators show a fall in disc fraction and a rise in bulge fraction among larger galaxies.Comment: 24 pages, 20 figures, MNRAS accepte

Cellular and Molecular Mechanisms of Fungal β-(1→6)-Glucan in Macrophages

Over the last 40-yr, the majority of research on glucans has focused on β-(1→3)-glucans. Recent studies indicate that β-(1→6)-glucans may be even more potent immune modulators than β-(1→3)-glucans. Mechanisms by which β-(1→6)-glucans are recognized and modulate immunity are unknown. In this study, we examined the interaction of purified water-soluble β-(1→6)-glucans with macrophage cell lines and primary peritoneal macrophages and the cellular and molecular consequences of this interaction. Our results indicate the existence of a specific β-(1→6)-glucan receptor that internalizes the glucan ligand via a clathrin-dependent mechanism. We show that the known β-(1→3)-glucans receptors are not responsible for β-(1→6)-glucan recognition and interaction. The receptor-ligand uptake/interaction has an apparent dissociation constant (KD) of ∼4-μM, and was associated with phosphorylation of ERK and JNK but not Iκ-α or p38. Our results indicate that macrophage interaction with β-(1→6)-glucans may lead to modulation of genes associated with anti-fungal immunity and recruitment/activation of neutrophils. In summary, we show that macrophages specifically bind and internalize β-(1→6)-glucans followed by activation of intracellular signaling and modulation of anti-fungal immune response-related gene regulation. Thus, we conclude that the interaction between innate immunity and β-(1→6)-glucans may play an important role in shaping the anti-fungal immune response

The DEEP2 Galaxy Redshift Survey: Mean Ages and Metallicities of Red Field Galaxies at z ~ 0.9 from Stacked Keck/DEIMOS Spectra

As part of the DEEP2 galaxy redshift survey, we analyze absorption line strengths in stacked Keck/DEIMOS spectra of red field galaxies with weak to no emission lines, at redshifts 0.7 <= z <= 1. Comparison with models of stellar population synthesis shows that red galaxies at z ~ 0.9 have mean luminosity-weighted ages of the order of only 1 Gyr and at least solar metallicities. This result cannot be reconciled with a scenario where all stars evolved passively after forming at very high z. Rather, a significant fraction of stars can be no more than 1 Gyr old, which means that star formation continued to at least z ~ 1.2. Furthermore, a comparison of these distant galaxies with a local SDSS sample, using stellar populations synthesis models, shows that the drop in the equivalent width of Hdelta from z ~ 0.9 to 0.1 is less than predicted by passively evolving models. This admits of two interpretations: either each individual galaxy experiences continuing low-level star formation, or the red-sequence galaxy population from z ~ 0.9 to 0.1 is continually being added to by new galaxies with younger stars.Comment: A few typos were corrected and numbers in Table 1 were revise

Similarity thresholds used in DNA sequence assembly from short reads can reduce the comparability of population histories across species

Comparing inferences among datasets generated using short read sequencing may provide insight into the concerted impacts of divergence, gene flow and selection across organisms, but comparisons are complicated by biases introduced during dataset assembly. Sequence similarity thresholds allow the de novo assembly of short reads into clusters of alleles representing different loci, but the resulting datasets are sensitive to both the similarity threshold used and to the variation naturally present in the organism under study. Thresholds that require high sequence similarity among reads for assembly (stringent thresholds) as well as highly variable species may result in datasets in which divergent alleles are lost or divided into separate loci (‘over-splitting’), whereas liberal thresholds increase the risk of paralogous loci being combined into a single locus (‘under-splitting’). Comparisons among datasets or species are therefore potentially biased if different similarity thresholds are applied or if the species differ in levels of within-lineage genetic variation. We examine the impact of a range of similarity thresholds on assembly of empirical short read datasets from populations of four different non-model bird lineages (species or species pairs) with different levels of genetic divergence. We find that, in all species, stringent similarity thresholds result in fewer alleles per locus than more liberal thresholds, which appears to be the result of high levels of over-splitting. The frequency of putative under-splitting, conversely, is low at all thresholds. Inferred genetic distances between individuals, gene tree depths, and estimates of the ancestral mutation-scaled effective population size (θ) differ depending upon the similarity threshold applied. Relative differences in inferences across species differ even when the same threshold is applied, but may be dramatically different when datasets assembled under different thresholds are compared. These differences not only complicate comparisons across species, but also preclude the application of standard mutation rates for parameter calibration. We suggest some best practices for assembling short read data to maximize comparability, such as using more liberal thresholds and examining the impact of different thresholds on each dataset

Does solar irradiation drive community assembly of vulture plumage microbiotas?

Abstract Background Stereotyped sunning behaviour in birds has been hypothesized to inhibit keratin-degrading bacteria but there is little evidence that solar irradiation affects community assembly and abundance of plumage microbiota. The monophyletic New World vultures (Cathartiformes) are renowned for scavenging vertebrate carrion, spread-wing sunning at roosts, and thermal soaring. Few avian species experience greater exposure to solar irradiation. We used 16S rRNA sequencing to investigate the plumage microbiota of wild individuals of five sympatric species of vultures in Guyana. Results The exceptionally diverse plumage microbiotas (631 genera of Bacteria and Archaea) were numerically dominated by bacterial genera resistant to ultraviolet (UV) light, desiccation, and high ambient temperatures, and genera known for forming desiccation-resistant endospores (phylum Firmicutes, order Clostridiales). The extremophile genera Deinococcus (phylum Deinococcus-Thermus) and Hymenobacter (phylum, Bacteroidetes), rare in vertebrate gut microbiotas, accounted for 9.1% of 2.7 million sequences (CSS normalized and log2 transformed). Five bacterial genera known to exhibit strong keratinolytic capacities in vitro (Bacillus, Enterococcus, Pseudomonas, Staphylococcus, and Streptomyces) were less abundant (totaling 4%) in vulture plumage. Conclusions Bacterial rank-abundance profiles from melanized vulture plumage have no known analog in the integumentary systems of terrestrial vertebrates. The prominence of UV-resistant extremophiles suggests that solar irradiation may play a significant role in the assembly of vulture plumage microbiotas. Our results highlight the need for controlled in vivo experiments to test the effects of UV on microbial communities of avian plumage

Irreversible transformation of ferromagnetic ordered stripe domains in single-shot IR pump - resonant X-ray scattering probe experiments

The evolution of a magnetic domain structure upon excitation by an intense, femtosecond Infra-Red (IR) laser pulse has been investigated using single-shot based time-resolved resonant X-ray scattering at the X-ray Free Electron laser LCLS. A well-ordered stripe domain pattern as present in a thin CoPd alloy film has been used as prototype magnetic domain structure for this study. The fluence of the IR laser pump pulse was sufficient to lead to an almost complete quenching of the magnetization within the ultrafast demagnetization process taking place within the first few hundreds of femtoseconds following the IR laser pump pulse excitation. On longer time scales this excitation gave rise to subsequent irreversible transformations of the magnetic domain structure. Under our specific experimental conditions, it took about 2 nanoseconds before the magnetization started to recover. After about 5 nanoseconds the previously ordered stripe domain structure had evolved into a disordered labyrinth domain structure. Surprisingly, we observe after about 7 nanoseconds the occurrence of a partially ordered stripe domain structure reoriented into a novel direction. It is this domain structure in which the sample's magnetization stabilizes as revealed by scattering patterns recorded long after the initial pump-probe cycle. Using micro-magnetic simulations we can explain this observation based on changes of the magnetic anisotropy going along with heat dissipation in the film.Comment: 16 pages, 6 figure

Potential strategies for strengthening surveillance of lymphatic filariasis in American Samoa after mass drug administration: reducing ‘number needed to test’ by targeting older age groups, hotspots, and household members of infected persons

Under the Global Programme to Eliminate Lymphatic Filariasis (LF), American Samoa conducted mass drug administration (MDA) from 2000–2006. Despite passing Transmission Assessment Surveys (TAS) in 2011/2012 and 2015, American Samoa failed TAS-3 in 2016, with antigen (Ag) prevalence of 0.7% (95%CI 0.3–1.8%) in 6–7 year-olds. A 2016 community survey (Ag prevalence 6.2% (95%CI 4.4–8.5%) in age ≥8 years) confirmed resurgence. Using data from the 2016 survey, this study aims to i) investigate antibody prevalence in TAS-3 and the community survey, ii) identify risk factors associated with being seropositive for Ag and anti-filarial antibodies, and iii) compare the efficiency of different sampling strategies for identifying seropositive persons in the post-MDA setting. Antibody prevalence in TAS-3 (n = 1143) were 1.6% for Bm14 (95%CI 0.9–2.9%), 7.9% for Wb123 (95%CI 6.4–9.6%), and 20.2% for Bm33 (95%CI 16.7–24.3%); and in the community survey (n = 2507), 13.9% for Bm14 (95%CI 11.2–17.2%), 27.9% for Wb123 (95%CI 24.6–31.4%), and 47.3% for Bm33 (95%CI 42.1–52.6%). Multivariable logistic regression was used to identify risk factors for being seropositive for Ag and antibodies. Higher Ag prevalence was found in males (adjusted odds ratio [aOR] 3.01), age ≥18 years (aOR 2.18), residents of Fagali’i (aOR 15.81), and outdoor workers (aOR 2.61). Ag prevalence was 20.7% (95%CI 9.7–53.5%) in households of Ag-positive children identified in TAS-3. We used NNTestav (average number needed to test to identify one positive) to compare the efficiency of the following strategies for identifying persons who were seropositive for Ag and each antibody: i) TAS of 6–7 year-old children, ii) population representative surveys of older age groups, and iii) targeted surveillance of subpopulations at higher risk of being seropositive (older ages, householders of Ag-positive TAS children, and known hotspots). For Ag, NNTestav ranged from 142.5 for TAS, to <5 for households of index children. NNTestav was lower in older ages, and highest for Ag, followed by Bm14, Wb123 and Bm33 antibodies. We propose a multi-stage surveillance strategy, starting with population-representative sampling (e.g. TAS or population representative survey of older ages), followed by strategies that target subpopulations and/or locations with low NNTestav. This approach could potentially improve the efficiency of identifying remaining infected persons and residual hotspots. Surveillance programs should also explore the utility of antibodies as indicators of transmission

Positive impact of pre-stroke surgery on survival following transient focal ischemia in hypertensive rats

We describe a positive influence of pre-stroke surgery on recovery and survival in a commonly used experimental stroke model. Two groups of male, stroke-prone spontaneously hypertensive rats (SHRSPs) underwent transient middle cerebral artery occlusion (tMCAO). Group 1 underwent the procedure without any prior intervention whilst group 2 had an additional general anaesthetic 6 days prior to tMCAO for a cranial burrhole and durotomy. Post-stroke recovery was assessed using a 32 point neurological deficit score and tapered beam walk and infarct volume determined from haematoxylin–eosin stained sections. In group 2 survival was 92% (n = 12) versus 67% in group 1 (n = 18). In addition, post-tMCAO associated weight loss was significantly reduced in group 2. There was no significant difference between the two groups in experimental outcomes: infarct volume (Group 1 317 ± 18.6 mm&lt;sup&gt;3&lt;/sup&gt; versus Group 2 332 ± 20.4 mm&lt;sup&gt;3&lt;/sup&gt;), and serial (day 0–14 post-tMCAO) neurological deficit scores and tapered-beam walk test. Drilling a cranial burrhole under general anaesthesia prior to tMCAO in SHRSP reduced mortality and gave rise to infarct volumes and neurological deficits similar to those recorded in surviving Group 1 animals. This methodological refinement has significant implications for animal welfare and group sizes required for intervention studies