Multi-frequency study of a new Fe-rich supernova remnant in the Large Magellanic Cloud, MCSNR J0508-6902

We present a detailed radio, X-ray and optical study of a newly discovered Large Magellanic Cloud (LMC) supernova remnant (SNR) which we denote MCSNR J0508-6902. Observations from the Australian Telescope Compact Array (ATCA) and the $\textit{XMM-Newton}$ X-ray observatory are complemented by deep H$\alpha$ images and Anglo Australian Telescope AAOmega spectroscopic data to study the SNR shell and its shock-ionisation. Archival data at other wavelengths are also examined. The remnant follows a filled-in shell type morphology in the radio-continuum and has a size of $\sim$74 pc $\times$ 57 pc at the LMC distance. The X-ray emission exhibits a faint soft shell morphology with Fe-rich gas in its interior $-$ indicative of a Type Ia origin. The remnant appears to be mostly dissipated at higher radio-continuum frequencies leaving only the south-eastern limb fully detectable while in the optical it is the western side of the SNR shell that is clearly detected. The best-fit temperature to the shell X-ray emission ($kT = 0.41^{+0.05}_{-0.06}$ keV) is consistent with other large LMC SNRs. We determined an O/Fe ratio of $<21$ and an Fe mass of 0.5-1.8$~M_{\odot}$ in the interior of the remnant, both of which are consistent with the Type Ia scenario. We find an equipartition magnetic field for the remnant of $\sim$28 $\mu$G, a value typical of older SNRs and consistent with other analyses which also infer an older remnant

Development and pilot evaluation of a personalized decision support intervention for low risk prostate cancer patients.

ObjectivesDevelopment and pilot evaluation of a personalized decision support intervention to help men with early-stage prostate cancer choose among active surveillance, surgery, and radiation.MethodsWe developed a decision aid featuring long-term survival and side effects data, based on focus group input and stakeholder endorsement. We trained premedical students to administer the intervention to newly diagnosed men with low-risk prostate cancer seen at the University of California, San Francisco. Before the intervention, and after the consultation with a urologist, we administered the Decision Quality Instrument for Prostate Cancer (DQI-PC). We hypothesized increases in two knowledge items from the DQI-PC: How many men diagnosed with early-stage prostate cancer will eventually die of prostate cancer? How much would waiting 3&nbsp;months to make a treatment decision affect chances of survival? Correct answers were: "Most will die of something else" and "A little or not at all."ResultsThe development phase involved 6 patients, 1 family member, 2 physicians, and 5 other health care providers. In our pilot test, 57 men consented, and 44 received the decision support intervention and completed knowledge surveys at both timepoints. Regarding the two knowledge items of interest, before the intervention, 35/56 (63%) answered both correctly, compared to 36/44 (82%) after the medical consultation (P&nbsp;=&nbsp;.04 by chi-square test).ConclusionsThe intervention was associated with increased patient knowledge. Data from this pilot have guided the development of a larger scale randomized clinical trial to improve decision quality in men with prostate cancer being treated in community settings

First release of the IPHAS catalogue of new extended planetary nebulae

Date of Acceptance: 30/06/2014We present the first results of our search for new, extended planetary nebulae (PNe) based on careful, systematic, visual scrutiny of the imaging data from the Isaac Newton Telescope Photometric Ha Survey of the Northern Galactic plane (IPHAS). The newly uncovered PNe will help to improve the census of this important population of Galactic objects that serve as key windows into the late-stage evolution of low- to intermediate-mass stars. They will also facilitate study of the faint end of the ensemble Galactic PN luminosity function. The sensitivity and coverage of IPHAS allows PNe to be found in regions of greater extinction in the Galactic plane and/or those PNe in a more advanced evolutionary state and at larger distances compared to the general Galactic PN population. Using a set of newly revised optical diagnostic diagrams in combination with access to a powerful, new, multiwavelength imaging data base, we have identified 159 true, likely and possible PNe for this first catalogue release. The ability of IPHAS to unveil PNe at low Galactic latitudes and towards the Galactic Anticentre, compared to previous surveys, makes this survey an ideal tool to contribute to the improvement of our knowledge of the whole Galactic PN population.Peer reviewe

XMMU J0541.8-6659, a new supernova remnant in the Large Magellanic Cloud

The high sensitivity of the XMM-Newton instrumentation offers the opportunity to study faint and extended sources in the Milky Way and nearby galaxies such as the Large Magellanic Cloud (LMC) in detail. The ROSAT PSPC survey of the LMC has revealed more than 700 X-ray sources, among which there are 46 supernova remnants (SNRs) and candidates. We have observed the field around one of the most promising SNR candidates in the ROSAT PSPC catalogue, labelled [HP99] 456 with XMM-Newton, to determine its nature. We investigated the XMM-Newton data along with new radio-continuum, near infrared and optical data. In particular, spectral and morphological studies of the X-ray and radio data were performed. The X-ray images obtained in different energy bands reveal two different structures. Below 1.0 keV the X-ray emission shows the shell-like morphology of an SNR with a diameter of ~73 pc, one of the largest known in the LMC. For its thermal spectrum we estimate an electron temperature of (0.49 +/- 0.12)keV assuming non-equilibrium ionisation. The X-ray images above 1.0 keV reveal a less extended source within the SNR emission, located ~1' west of the centre of the SNR and coincident with bright point sources detected in radio-continuum. This hard component has an extent of 0.9' (i.e. ~13 pc at a distance of ~50 kpc) and a non-thermal spectrum. The hard source coincides in position with the ROSAT source [HP99] 456 and shows an indication for substructure. We firmly identify a new SNR in the LMC with a shell-like morphology and a thermal spectrum. Assuming the SNR to be in the Sedov phase yields an age of ~23 kyr. We explore possible associations of the hard non-thermal emitting component with a pulsar wind nebula (PWN) or background active galactic nuclei (AGN).Comment: 8 pages, 7 figures, accepted for publication in Astronomy and Astrophysic

The perspectives of natural deep eutectic solvents in agri-food sector

Plant science

Hybrid assembly with long and short reads improves discovery of gene family expansions

BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. RESULTS: Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. CONCLUSION: Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation

Assessment Results of Fluid-Structure Interaction Numerical Simulation Using Fuzzy Logic

A fuzzy approximation concept is applied in order to predict results of coupled computational structure mechanics and computational fluid dynamics while solving a problem of steady incompressible gas flow through thermally loaded rectangular thin-walled channel. Channel wall deforms into wave-type shapes depending on thermal load and fluid inlet velocity inducing the changes of fluid flow accordingly. A set of fluid-structure interaction numerical tests have been defined by varying the values of fluid inlet velocity, temperature of inner and outer surface of the channel wall, and numerical grid density. The unsteady Navier-Stokes equations are numerically solved using an element-based finite volume method and second order backward Euler discretization scheme. The structural model is solved by finite element method including geometric and material non-linearities. The implicit two-way iterative code coupling, partitioned solution approach, were used while solving these numerical tests. Results of numerical analysis indicate that gravity and pressure distribution inside the channel contributes to triggering the shape of deformation. In the inverse problem, the results of fluid-structure interaction numerical simulations formed a database of input variables for development fuzzy logic based models considering downstream pressure drop and maximum stresses as the objective functions. Developed fuzzy models predicted targeting results within a reasonable accuracy limit at lower computation cost compared to series of fluid-structure interaction numerical calculations. Smaller relative difference were obtained when calculating the values of pressure drop then maximal stresses indicating that transfer function influence on output values have to be additionally investigated

Development of mPing-based activation tags for crop insertional mutagenesis

Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system

Multi-frequency study of the Large Magellanic Cloud Supernova Remnant J0529-6653 near Pulsar B0529-66

We report the ATCA and ROSAT detection of Supernova Remnant (SNR) J0529--6653 in the Large Magellanic Cloud (LMC) which is positioned in the projected vicinity of the known radio pulsar PSR B0529-66. In the radio-continuum frequencies, this LMC object follows a typical SNR structure of a shell morphology with brightened regions in the south-west. It exhibits an almost circular shape of D=33 x 31 pc (1 pc uncertainty in each direction) and radio spectral index of alpha=-0.68$+-$0.03 - typical for mid-age SNRs. We also report detection of polarised regions with a peak value of 17+-7% at 6 cm. An investigation of ROSAT images produced from merged PSPC data reveals the presence of extended X-ray emission coincident with the radio emission of the SNR. In X-rays, the brightest part is in the north-east. We discuss various scenarios in regards to the SNR-PSR association with emphasis on the large age difference, lack of a pulsar trail and no prominent point-like radio or X-ray source.Comment: 8 pages, 9 figures, accepted for publication in MNRA