New filamentary remnant radio emission and duty cycle constraints in the radio galaxy NGC 6086

Radio galaxies are a subclass of active galactic nuclei in which accretion onto the supermassive black hole releases energy via relativistic jets. The jets are not constantly active throughout the life of the host galaxy and alternate between active and quiescent phases. Remnant radio galaxies are detected during a quiescent phase and define a class of unique sources to constrain the AGN duty cycle. We present, a spatially resolved radio analysis of the radio galaxy associated with NGC 6086 and constraints on the spectral age of the diffuse emission to investigate the duty cycle and evolution of the source. We use three new low-frequency, high-sensitivity observations, performed with the Low Frequency Array at 144 MHz and with the upgraded Giant Metrewave Radio Telescope at 400 MHz and 675 MHz. To these, we add two Very Large Array archival observations at 1400 and 4700 MHz. In the new observations, we detect a second pair of larger lobes and three regions with a filamentary morphology. We analyse the spectral index trend in the inner remnant lobes and see systematic steeper values at the lower frequencies compared to the GHz ones. Steeper spectral indices are found in the newly detected outer lobes (up to 2.1), as expected if they trace a previous phase of activity of the AGN. However, the differences between the spectra suggest different dynamical evolution within the intragroup medium during their expansion and/or different magnetic field values. We place constraints on the age of the inner and outer lobes and derive the duty cycle of the source. This results in a total active time of $\sim$39%. The filamentary structures have a steep spectral index ($\sim$1) without any spectral index trend and only one of them shows a steepening in the spectrum. Their origin is not yet clear, but they may have formed due to the compression of the plasma or due to magnetic field substructures

Pre-symptomatic modified phytohormone profile is associated with lower phytoplasma titres in an Arabidopsis seor1ko line

The proteins AtSEOR1 and AtSEOR2 occur as conjugates in the form of filaments in sieve elements of Arabidopsis thaliana. A reduced phytoplasma titre found in infected defective-mutant Atseor1ko plants in previous work raised the speculation that non-conjugated SEOR2 is involved in the phytohormone-mediated suppression of Chrysanthemum Yellows (CY)-phytoplasma infection transmitted by Euscelidius variegatus (Ev). This early and long-lasting SEOR2 impact was revealed in Atseor1ko plants by the lack of detectable phytoplasmas at an early stage of infection (symptomless plants) and a lower phytoplasma titre at a later stage (fully symptomatic plants). The high insect survival rate on Atseor1ko line and the proof of phytoplasma infection at the end of the acquisition access period confirmed the high transmission efficiency of CY-phytoplasma by the vectors. Transmission electron microscopy analysis ruled out a direct role of SE filament proteins in physical phytoplasma containment. Time-correlated HPLC\u2013MS/MS-based phytohormone analyses revealed increased jasmonate levels in midribs of Atseor1ko plants at an early stage of infection and appreciably enhanced levels of indole acetic acid and abscisic acid at the early and late stages. Effects of Ev-probing on phytohormone levels was not found. The results suggest that SEOR2 interferes with phytohormonal pathways in Arabidopsis midrib tissues in order to establish early defensive responses to phytoplasma infection

A MeerKAT-meets-LOFAR study of Abell 1413: a moderately disturbed non-cool-core cluster hosting a ∼500\sim 500 kpc 'mini'-halo

Many relaxed cool-core clusters host diffuse radio emission on scales of hundreds of kiloparsecs: mini-haloes. However, the mechanism responsible for generating them, as well as their connection with central active galactic nuclei, is elusive and many questions related to their physical properties and origins remain unanswered. This paper presents new radio observations of the galaxy cluster Abell 1413 performed with MeerKAT (L-band; 872 to 1712 MHz) and LOFAR HBA (120 to 168 MHz) as part of a statistical and homogeneous census of mini-haloes. Abell 1413 is unique among mini-halo clusters as it is a moderately-disturbed non-cool-core cluster. Our study reveals an asymmetric mini-halo up to 584 kpc in size at 1283 MHz, twice as large as first reported at similar frequencies. The spectral index is flatter than previously reported, with an integrated value of $\alpha = -1.01 \pm 0.06$, shows significant spatial variation, and a tentative radial steepening. We studied the point-to-point X-ray/radio surface brightness correlation to investigate the thermal/non-thermal connection: our results show a strong connection between these components, with a super-linear slope of $b = 1.63 \pm 0.10$ at 1283 MHz and $b = 1.20 \pm 0.12$ at 145 MHz. We also explore the X-ray surface brightness/radio spectral index correlation, finding a slope of $b = 0.59 \pm 0.11$. Both investigations support the evidence of spectral steepening. Finally, in the context of understanding the particle acceleration mechanism, we present a simple theoretical model which demonstrates that hybrid scenarios - secondary electrons (re-)accelerated by turbulence - reproduce a super-linear correlation slope.Comment: 19 pages, 11 figures, 4 tables. Accepted for publication in MNRA

Ionospheric Modelling using GPS to Calibrate the MWA. II : Regional ionospheric modelling using GPS and GLONASS to estimate ionospheric gradients

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Publications of the Astronomical Society of Australia (PASA), after peer review and technical editing by the publisher. The version of record is available on line at https://doi.org/10.1017/pasa.2016.22 COPYRIGHT: © Astronomical Society of Australia 2016.We estimate spatial gradients in the ionosphere using the Global Positioning System (GPS) and GLONASS (Russian global navigation system) observations, utilising data from multiple GPS stations in the vicinity of Murchison Radio-astronomy Observatory (MRO). In previous work the ionosphere was characterised using a single-station to model the ionosphere as a single layer of fixed height and this was compared with ionospheric data derived from radio astronomy observations obtained from the Murchison Widefield Array (MWA). Having made improvements to our data quality (via cycle slip detection and repair) and incorporating data from the GLONASS system, we now present a multi-station approach. These two developments significantly improve our modelling of the ionosphere. We also explore the effects of a variable-height model. We conclude that modelling the small-scale features in the ionosphere that have been observed with the MWA will require a much denser network of Global Navigation Satellite System (GNSS) stations than is currently available at the MRO.Peer reviewe

Probing ionospheric structures using the LOFAR radio telescope

LOFAR is the LOw-Frequency Radio interferometer ARray located at midlatitude (52°53′N). Here we present results on ionospheric structures derived from 29 LOFAR nighttime observations during the winters of 2012/2013 and 2013/2014. We show that LOFAR is able to determine differential ionospheric total electron content values with an accuracy better than 0.001 total electron content unit = 1016m−2 over distances ranging between 1 and 100 km. For all observations the power law behavior of the phase structure function is confirmed over a long range of baseline lengths, between 1 and 80 km, with a slope that is, in general, larger than the 5/3 expected for pure Kolmogorov turbulence. The measured average slope is 1.89 with a one standard deviation spread of 0.1. The diffractive scale, i.e., the length scale where the phase variance is 1rad2, is shown to be an easily obtained single number that represents the ionospheric quality of a radio interferometric observation. A small diffractive scale is equivalent to high phase variability over the field of view as well as a short time coherence of the signal, which limits calibration and imaging quality. For the studied observations the diffractive scales at 150 MHz vary between 3.5 and 30 km. A diffractive scale above 5 km, pertinent to about 90% of the observations, is considered sufficient for the high dynamic range imaging needed for the LOFAR epoch of reionization project. For most nights the ionospheric irregularities were anisotropic, with the structures being aligned with the Earth magnetic field in about 60% of the observations

Understanding the radio relic emission in the galaxy cluster MACS J0717.5+3745: Spectral analysis

Radio relics are diffuse, extended synchrotron sources that originate from shock fronts generated during cluster mergers. The massive merging galaxy cluster MACS J0717.5+3745 hosts one of the more complex relics known to date. We present upgraded Giant Metrewave Radio Telescope band 3 (300-500 MHz) and band 4 (550-850 MHz) observations. These new observations, combined with published VLA and the new LOFAR HBA data, allow us to carry out a detailed, high spatial resolution spectral analysis of the relic over a broad range of frequencies. The integrated spectrum of the relic closely follows a power law between 144 MHz and 5.5 GHz with a mean spectral slope αâ€., =â€., -1.16†±â€ 0.03. Despite the complex morphology of this relic, its subregions and the other isolated filaments also follow power-law behaviors, and show similar spectral slopes. Assuming diffusive shock acceleration, we estimated a dominant Mach number of ∼3.7 for the shocks that make up the relic. A comparison with recent numerical simulations suggests that in the case of radio relics, the slopes of the integrated radio spectra are determined by the Mach number of the accelerating shock, with α nearly constant, namely between -1.13 and -1.17, for Mach numbers 3.5†-†4.0. The spectral shapes inferred from spatially resolved regions show curvature, we speculate that the relic is inclined along the line of sight. The locus of points in the simulated color-color plots changes significantly with the relic viewing angle. We conclude that projection effects and inhomogeneities in the shock Mach number dominate the observed spectral properties of the relic in this complex system. Based on the new observations we raise the possibility that the relic and a narrow-angle-tailed radio galaxy are two different structures projected along the same line of sight

Meta-analysis of gene expression microarrays with missing replicates

<p>Abstract</p> <p>Background</p> <p>Many different microarray experiments are publicly available today. It is natural to ask whether different experiments for the same phenotypic conditions can be combined using meta-analysis, in order to increase the overall sample size. However, some genes are not measured in all experiments, hence they cannot be included or their statistical significance cannot be appropriately estimated in traditional meta-analysis. Nonetheless, these genes, which we refer to as <it>incomplete genes</it>, may also be informative and useful.</p> <p>Results</p> <p>We propose a meta-analysis framework, called "Incomplete Gene Meta-analysis", which can include incomplete genes by imputing the significance of missing replicates, and computing a meta-score for every gene across all datasets. We demonstrate that the incomplete genes are worthy of being included and our method is able to appropriately estimate their significance in two groups of experiments. We first apply the <it>Incomplete Gene Meta-analysis </it>and several comparable methods to five breast cancer datasets with an identical set of probes. We simulate incomplete genes by randomly removing a subset of probes from each dataset and demonstrate that our method consistently outperforms two other methods in terms of their false discovery rate. We also apply the methods to three gastric cancer datasets for the purpose of discriminating diffuse and intestinal subtypes.</p> <p>Conclusions</p> <p>Meta-analysis is an effective approach that identifies more robust sets of differentially expressed genes from multiple studies. The incomplete genes that mainly arise from the use of different platforms may also have statistical and biological importance but are ignored or are not appropriately involved by previous studies. Our Incomplete Gene Meta-analysis is able to incorporate the incomplete genes by estimating their significance. The results on both breast and gastric cancer datasets suggest that the highly ranked genes and associated GO terms produced by our method are more significant and biologically meaningful according to the previous literature.</p

Nicotine Protects Kidney from Renal Ischemia/Reperfusion Injury through the Cholinergic Anti-Inflammatory Pathway

Kidney ischemia/reperfusion injury (I/R) is characterized by renal dysfunction and tubular damages resulting from an early activation of innate immunity. Recently, nicotine administration has been shown to be a powerful inhibitor of a variety of innate immune responses, including LPS-induced toxaemia. This cholinergic anti-inflammatory pathway acts via the α7 nicotinic acetylcholine receptor (α7nAChR). Herein, we tested the potential protective effect of nicotine administration in a mouse model of renal I/R injury induced by bilateral clamping of kidney arteries. Renal function, tubular damages and inflammatory response were compared between control animals and mice receiving nicotine at the time of ischemia. Nicotine pretreatment protected mice from renal dysfunction in a dose-dependent manner and through the α7nAChR, as attested by the absence of protection in α7nAChR-deficient mice. Additionally, nicotine significantly reduced tubular damages, prevented neutrophil infiltration and decreased productions of the CXC-chemokine KC, TNF-α and the proinflammatory high-mobility group box 1 protein. Reduced tubular damage in nicotine pre-treated mice was associated with a decrease in tubular cell apoptosis and proliferative response as attested by the reduction of caspase-3 and Ki67 positive cells, respectively. All together, these data highlight that nicotine exerts a protective anti-inflammatory effect during kidney I/R through the cholinergic α7nAChR pathway. In addition, this could provide an opportunity to overcome the effect of surgical cholinergic denervation during kidney transplantation

Susceptibility to COPD:Differential Proteomic Profiling after Acute Smoking

Cigarette smoking is the main risk factor for COPD (Chronic Obstructive Pulmonary Disease), yet only a subset of smokers develops COPD. Family members of patients with severe early-onset COPD have an increased risk to develop COPD and are therefore defined as "susceptible individuals". Here we perform unbiased analyses of proteomic profiles to assess how "susceptible individuals" differ from age-matched "non-susceptible individuals" in response to cigarette smoking. Epithelial lining fluid (ELF) was collected at baseline and 24 hours after smoking 3 cigarettes in young individuals susceptible or non-susceptible to develop COPD and older subjects with established COPD. Controls at baseline were older healthy smoking and non-smoking individuals. Five samples per group were pooled and analysed by stable isotope labelling (iTRAQ) in duplicate. Six proteins were selected and validated by ELISA or immunohistochemistry. After smoking, 23 proteins increased or decreased in young susceptible individuals, 7 in young non-susceptible individuals, and 13 in COPD in the first experiment; 23 proteins increased or decreased in young susceptible individuals, 32 in young non-susceptible individuals, and 11 in COPD in the second experiment. SerpinB3 and Uteroglobin decreased after acute smoke exposure in young non-susceptible individuals exclusively, whereas Peroxiredoxin I, S100A9, S100A8, ALDH3A1 (Aldehyde dehydrogenase 3A1) decreased both in young susceptible and non-susceptible individuals, changes being significantly different between groups for Uteroglobin with iTRAQ and for Serpin B3 with iTRAQ and ELISA measures. Peroxiredoxin I, SerpinB3 and ALDH3A1 increased in COPD patients after smoking. We conclude that smoking induces a differential protein response in ELF of susceptible and non-susceptible young individuals, which differs from patients with established COPD. This is the first study applying unbiased proteomic profiling to unravel the underlying mechanisms that induce COPD. Our data suggest that SerpinB3 and Uteroglobin could be interesting proteins in understanding the processes leading to COPD