ImpZ: a new photometric redshift code for galaxies and quasars

We present a combined galaxy-quasar approach to template-fitting photometric redshift techniques and show the method to be a powerful one. The code (ImpZ) is presented, developed and applied to two spectroscopic redshift catalogues, namely the Isaac Newton Telescope Wide Angle Survey ELAIS N1 and N2 fields and the Chandra Deep Field North. In particular, optical size information is used to improve the redshift determination. The success of the code is shown to be very good with Delta z/(1+z) constrained to within 0.1 for 92 per cent of the galaxies in our sample. The extension of template-fitting to quasars is found to be reasonable with Delta z/(1+z) constrained to within 0.25 for 68 per cent of the quasars in our sample. Various template extensions into the far-UV are also tested.Comment: 21 pages. MNRAS in press. Minor alterations to match MNRAS final proo

The ATLAS 5.5 GHz survey of the Extended Chandra Deep Field South: Catalogue, Source Counts and Spectral Indices

Star forming galaxies are thought to dominate the sub-mJy radio population, but recent work has shown that low luminosity AGN can still make a significant contribution to the faint radio source population. Spectral indices are an important tool for understanding the emission mechanism of the faint radio sources. We have observed the extended Chandra Deep Field South at 5.5 GHz using a mosaic of 42 pointings with the Australia Telescope Compact Array (ATCA). Our image reaches an almost uniform sensitivity of ~12 microJy rms over 0.25 deg^2 with a restoring beam of 4.9 x 2.0 arcsec, making it one of the deepest 6cm surveys to date. We present the 5.5 GHz catalogue and source counts from this field. We take advantage of the large amounts of ancillary data in this field to study the 1.4 to 5.5 GHz spectral indices of the sub-mJy population. For the full 5.5 GHz selected sample we find a flat median spectral index, alpha_med = -0.40, which is consistent with previous results. However, the spectral index appears to steepen at the faintest flux density levels (S_{5.5 GHz} < 0.1 mJy), where alpha_med = -0.68. We performed stacking analysis of the faint 1.4 GHz selected sample (40 < S_{1.4 GHz} < 200 microJy) and also find a steep average spectral index, alpha = -0.8, consistent with synchrotron emission. We find a weak trend of steepening spectral index with redshift. Several young AGN candidates are identified using spectral indices, suggesting Gigahertz Peaked Spectrum (GPS) sources are as common in the mJy population as they are at Jy levels.Comment: 18 pages, 16 figures, accepted for publication in MNRA

Optical and Infrared Diagnostics of SDSS galaxies in the SWIRE Survey

We present the rest-frame optical and infrared colours of a complete sample of 1114 z<0.3 galaxies from the Spitzer Wide-area InfraRed Extragalactic Legacy Survey (SWIRE) and the Sloan Digital Sky Survey (SDSS). We discuss the optical and infrared colours of our sample and analyse in detail the contribution of dusty star-forming galaxies and AGN to optically selected red sequence galaxies. We propose that the optical (g-r) colour and infrared log(L_{24}/L_{3.6}) colour of galaxies in our sample are determined primarily by a bulge-to-disk ratio. The (g-r) colour is found to be sensitive to the bulge-to-disk ratio for disk-dominated galaxies, whereas the log(L_{24}/L_{3.6}) colour is more sensitive for bulge-dominated systems. We identify ~18% (195 sources) of our sample as having red optical colours and infrared excess. Typically, the infrared luminosities of these galaxies are found to be at the high end of star-forming galaxies with blue optical colours. Using emission line diagnostic diagrams, 78 are found to have an AGN contribution, and 117 are identified as star-forming systems. The red (g-r) colour of the star-forming galaxies could be explained by extinction. However, their high optical luminosities cannot. We conclude that they have a significant bulge component. The number densities of optically red star-forming galaxies are found to correspond to ~13% of the total number density of our sample. In addition, these systems contribute ~13% of the total optical luminosity density, and 28% of the total infrared luminosity density of our SWIRE/SDSS sample. These objects may reduce the need for "dry-mergers".Comment: 14 pages, 8 figures, 4 tables. Accepted for publication in MNRA

Lack of a functioning P2X7 receptor leads to increased susceptibility to toxoplasmic ileitis

Background: Oral infection of C57BL/6J mice with the protozoan parasite Toxoplasma gondii leads to a lethal inflammatory ileitis. Principal Findings: Mice lacking the purinergic receptor P2X7R are acutely susceptible to toxoplasmic ileitis, losing significantly more weight than C57BL/6J mice and exhibiting much greater intestinal inflammatory pathology in response to infection with only 10 cysts of T. gondii. This suscep-tibility is not dependent on the ability of P2X7R-deficient mice to control the parasite, which they accomplish just as efficiently as C57BL/6J mice. Rather, susceptibility is associated with elevated ileal concentrations of pro-inflammatory cytokines, reactive nitrogen interme-diates and altered regulation of elements of NFκB activation in P2X7R-deficient mice. Conclusions: Our data support the thesis that P2X7R, a well-documented activator of pro-inflammatory cytokine production, also plays an important role in the regulation of intestinal inflammation

Nematicidal effects of cysteine proteinases against sedentary plant parasitic nematodes

Cysteine proteinases from the fruit and latex of plants, such as papaya, pineapple and fig, have previously been shown to have substantial anthelmintic efficacy, in vitro and in vivo, against a range of animal parasitic nematodes. In this paper, we describe the in vitro effects of these plant extracts against 2 sedentary plant parasitic nematodes of the genera Meloidogyne and Globodera. All the plant extracts examined caused digestion of the cuticle and decreased the activity of the tested nematodes. The specific inhibitor of cysteine proteinases, E-64, blocked this activity completely, indicating that it was essentially mediated by cysteine proteinases. In vitro, plant cysteine proteinases are active against second-stage juveniles of M. incognita and M. javanica, and some cysteine proteinases also affect the second-stage juveniles of Globodera rostochiensis. It is not known yet whether these plant extracts will interfere with, or prevent invasion of, host plants

Numerical simulations of stellar SiO maser variability. Investigation of the effect of shocks

A stellar hydrodynamic pulsation model has been combined with a SiO maser model in an attempt to calculate the temporal variability of SiO maser emission in the circumstellar envelope (CE) of a model AGB star. This study investigates whether the variations in local physical conditions brought about by shocks are the predominant contributing factor to SiO maser variability because, in this work, the radiative part of the pump is constant. We find that some aspects of the variability are not consistent with a pump provided by shock-enhanced collisions alone. In these simulations, gas parcels of relatively enhanced SiO abundance are distributed in a model CE by a Monte Carlo method, at a single epoch of the stellar cycle. From this epoch on, Lagrangian motions of individual parcels are calculated according to the velocity fields encountered in the model CE during the stellar pulsation cycle. The potentially masing gas parcels therefore experience different densities and temperatures, and have varying line-of-sight velocity gradients throughout the stellar cycle, which may or may not be suitable to produce maser emission. At each epoch (separated by 16.6 days), emission lines from the parcels are combined to produce synthetic spectra and VLBI-type images. We report here the results for v=1, J=1-0 (43-GHz) and J=2-1 (86-GHz) masers.Comment: 16 pages, 8 figures, accepted by A&

Deep 1.1 mm-wavelength imaging of the GOODS-S field by AzTEC/ASTE - I. Source catalogue and number counts

[Abridged] We present the first results from a 1.1 mm confusion-limited map of the GOODS-S field taken with AzTEC on the ASTE telescope. We imaged a 270 sq. arcmin field to a 1\sigma depth of 0.48 - 0.73 mJy/beam, making this one of the deepest blank-field surveys at mm-wavelengths ever achieved. Although our GOODS-S map is extremely confused, we demonstrate that our source identification and number counts analyses are robust, and the techniques discussed in this paper are relevant for other deeply confused surveys. We find a total of 41 dusty starburst galaxies with S/N >= 3.5 within this uniformly covered region, where only two are expected to be false detections. We derive the 1.1mm number counts from this field using both a "P(d)" analysis and a semi-Bayesian technique, and find that both methods give consistent results. Our data are well-fit by a Schechter function model with (S', N(3mJy), \alpha) = (1.30+0.19 mJy, 160+27 (mJy/deg^2)^(-1), -2.0). Given the depth of this survey, we put the first tight constraints on the 1.1 mm number counts at S(1.1mm) = 0.5 mJy, and we find evidence that the faint-end of the number counts at S(850\mu m) < 2.0 mJy from various SCUBA surveys towards lensing clusters are biased high. In contrast to the 870 \mu m survey of this field with the LABOCA camera, we find no apparent under-density of sources compared to previous surveys at 1.1 mm. Additionally, we find a significant number of SMGs not identified in the LABOCA catalogue. We find that in contrast to observations at wavelengths < 500 \mu m, MIPS 24 \mu m sources do not resolve the total energy density in the cosmic infrared background at 1.1 mm, demonstrating that a population of z > 3 dust-obscured galaxies that are unaccounted for at these shorter wavelengths potentially contribute to a large fraction (~2/3) of the infrared background at 1.1 mm.Comment: 21 pages, 9 figures. Accepted to MNRAS

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

This article is made available for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing.BACKGROUND: Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. METHODS: We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. RESULTS: We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). CONCLUSIONS: An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease

Lung carcinoma with hypertrophic osteoarthropathy in a teenager

Hypertrophic osteoarthropathy (HOA) characterised by arthralgia, clubbing and periosteal proliferation of long bones, is rarely encountered in children and adolescents. Whereas in adults over 80% of cases are associated with malignancy, in children the majority of cases are due to non-neoplastic causes such as cystic fibrosis, bilary atresia and congenital heart disease. Up to 5% of adults with lung cancer demonstrate signs of HOA. However, lung cancer is extremely uncommon in children and young people. Here we report a case of lung adenocarcinoma in an 18 year old male associated with HOA present both at diagnosis and at subsequent disease progression