The Emergence of the Infrared transient VVV-WIT-06

We report the discovery of an enigmatic large-amplitude (ΔKs> 10.5 mag) transient event in near-IR data obtained by the VISTA Variables in the Via Lactea (VVV) ESO Public Survey. The object (designated VVV-WIT-06) is located at R.A. = 17:07:18.917, decl. = -39:06:26.45 (J2000), corresponding to Galactic coordinates l = 347.14539, b = 0.88522. It exhibits a clear eruption, peaking at Ks = 9 mag during 2013 July and fading to Ks ~ 16.5 in 2017. Our late near-IR spectra show post-outburst emission lines, including some broad emission lines (upward of {FWHM} ~ 3000 k/s). We estimate a total extinction of A_V=10--15 mag in the surrounding field, and no progenitor was observed in ZYJHKs images obtained during 2010-2012 (down to Ks> 18.5 mag). Subsequent deep near-IR imaging and spectroscopy, in concert with the available multiband photometry, indicate that VVV-WIT-06 may be either: (I) the closest Type I SN observed in about 400 years, (II) an exotic high-amplitude nova that would extend the known realm of such objects, or (III) a stellar merger. In all of these cases, VVV-WIT-06 is a fascinating and curious astrophysical target under any of the scenarios considered.Peer reviewe

On the Progenitor System of Nova V2491 Cygni

Nova V2491 Cyg is one of just two detected pre-outburst in X-rays. The light curve of this nova exhibited a rare "re-brightening" which has been attributed by some as the system being a polar, whilst others claim that a magnetic WD is unlikely. By virtue of the nature of X-ray and spectroscopic observations the system has been proposed as a recurrent nova, however the adoption of a 0.1 day orbital period is generally seen as incompatible with such a system. In this research note we address the nature of the progenitor system and the source of the 0.1 day periodicity. Through the combination of Liverpool Telescope observations with published data and archival 2MASS data we show that V2491 Cyg, at a distance of 10.5 - 14 kpc, is likely to be a recurrent nova of the U Sco-class; containing a sub-giant secondary and an accretion disk, rather than accretion directly onto the poles. We show that there is little evidence, at quiescence, supporting a ~ 0.1 day periodicity, the variation seen at this stage is likely caused by flickering of a re-established accretion disk. We propose that the periodicity seen shortly after outburst is more likely related to the outburst rather than the - then obscured - binary system. Finally we address the distance to the system, and show that a significantly lower distance (~ 2 kpc) would result in a severely under-luminous outburst, and as such favour the larger distance and the recurrent nova scenario.Comment: 5 pages, 3 images, accepted for publication in A&A as a research not

Elemental Abundances in the Ejecta of Old Classical Novae from Late-Epoch Spitzer Spectra

We present Spitzer Space Telescope mid-infrared IRS spectra, supplemented by ground-based optical observations, of the classical novae V1974 Cyg, V382 Vel, and V1494 Aql more than 11, 8, and 4 years after outburst respectively. The spectra are dominated by forbidden emission from neon and oxygen, though in some cases, there are weak signatures of magnesium, sulfur, and argon. We investigate the geometry and distribution of the late time ejecta by examination of the emission line profiles. Using nebular analysis in the low density regime, we estimate lower limits on the abundances in these novae. In V1974 Cyg and V382 Vel, our observations confirm the abundance estimates presented by other authors and support the claims that these eruptions occurred on ONe white dwarfs. We report the first detection of neon emission in V1494 Aql and show that the system most likely contains a CO white dwarf.Comment: 22 pages, 12 figure

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434

Evaluation of methods for detecting conversion events in gene clusters

Background: Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods. Results: We designed a new method that simulates gene cluster evolution, including large-scale events of duplication, deletion, and conversion as well as small mutations. We used this simulation data to evaluate several different programs for detecting gene conversion events. Conclusions: Our evaluation identifies strengths and weaknesses of several methods for detecting gene conversion, which can contribute to more accurate analysis of gene cluster evolution

Diagnostic, prognostic and predictive value of cell-free miRNAs in prostate cancer : A systematic review

Publisher Copyright: © 2016 Endzeliņš et al.Prostate cancer, the second most frequently diagnosed cancer in males worldwide, is estimated to be diagnosed in 1.1 million men per year. Introduction of PSA testing substantially improved early detection of prostate cancer, however it also led to overdiagnosis and subsequent overtreatment of patients with an indolent disease. Treatment outcome and management of prostate cancer could be improved by the development of non-invasive biomarker assays that aid in increasing the sensitivity and specificity of prostate cancer screening, help to distinguish aggressive from indolent disease and guide therapeutic decisions. Prostate cancer cells release miRNAs into the bloodstream, where they exist incorporated into ribonucleoprotein complexes or extracellular vesicles. Later, cell-free miRNAs have been found in various other biofluids. The initial RNA sequencing studies suggested that most of the circulating cell-free miRNAs in healthy individuals are derived from blood cells, while specific disease-associated miRNA signatures may appear in the circulation of patients affected with various diseases, including cancer. This raised a hope that cell-free miRNAs may serve as non-invasive biomarkers for prostate cancer. Indeed, a number of cell-free miRNAs that potentially may serve as diagnostic, prognostic or predictive biomarkers have been discovered in blood or other biofluids of prostate cancer patients and need to be validated in appropriately designed longitudinal studies and clinical trials. In this review, we systematically summarise studies investigating cell-free miRNAs in biofluids of prostate cancer patients and discuss the utility of the identified biomarkers in various clinical scenarios. Furthermore, we discuss the possible mechanisms of miRNA release into biofluids and outline the biological questions and technical challenges that have arisen from these studies.publishersversionPeer reviewe

Proteomic Analysis of Fusarium solani Isolated from the Asian Longhorned Beetle, Anoplophora glabripennis

Wood is a highly intractable food source, yet many insects successfully colonize and thrive in this challenging niche. Overcoming the lignin barrier of wood is a key challenge in nutrient acquisition, but full depolymerization of intact lignin polymers has only been conclusively demonstrated in fungi and is not known to occur by enzymes produced by insects or bacteria. Previous research validated that lignocellulose and hemicellulose degradation occur within the gut of the wood boring insect, Anoplophora glabripennis (Asian longhorned beetle), and that a fungal species, Fusarium solani (ATCC MYA 4552), is consistently associated with the larval stage. While the nature of this relationship is unresolved, we sought to assess this fungal isolate's ability to degrade lignocellulose and cell wall polysaccharides and to extract nutrients from woody tissue. This gut-derived fungal isolate was inoculated onto a wood-based substrate and shotgun proteomics using Multidimensional Protein Identification Technology (MudPIT) was employed to identify 400 expressed proteins. Through this approach, we detected proteins responsible for plant cell wall polysaccharide degradation, including proteins belonging to 28 glycosyl hydrolase families and several cutinases, esterases, lipases, pectate lyases, and polysaccharide deacetylases. Proteinases with broad substrate specificities and ureases were observed, indicating that this isolate has the capability to digest plant cell wall proteins and recycle nitrogenous waste under periods of nutrient limitation. Additionally, several laccases, peroxidases, and enzymes involved in extracellular hydrogen peroxide production previously implicated in lignin depolymerization were detected. In vitro biochemical assays were conducted to corroborate MudPIT results and confirmed that cellulases, glycosyl hydrolases, xylanases, laccases, and Mn- independent peroxidases were active in culture; however, lignin- and Mn- dependent peroxidase activities were not detected While little is known about the role of filamentous fungi and their associations with insects, these findings suggest that this isolate has the endogenous potential to degrade lignocellulose and extract nutrients from woody tissue

A 17-gene Assay to Predict Prostate Cancer Aggressiveness in the Context of Gleason Grade Heterogeneity, Tumor Multifocality, and Biopsy Undersampling

avai lable at www.sciencedirect.com journal homepage: www.europeanurology.com Genomic Prostate Score Outcome measures and statistical analysis: The main outcome measures defining aggressive PCa were clinical recurrence, PCa death, and adverse pathology at prostatec-predictive of aggressClinical validation Clinical utility tomy. Cox proportional hazards regressionmodels were used to evaluate the association between gene expression and time to event end points. Results from the prostatectomy and biopsy studies were used to develop and lock a multigene-expression-based signature, called the Genomic Prostate Score (GPS); in the validation study, logistic regression was used to test the association between the GPS and pathologic stage and grade at prostatectomy. Decision-curve analysis and risk profileswere used together with clinical and pathologic characteristics to evaluate clinical utility. Results and limitations: Of the 732 candidate genes analyzed, 288 (39%) were found to predict clinical recurrence despite heterogeneity and multifocality, and 198 (27%) were ive disease after adjustment for prostate-specific antigen, GleasonArticle inf

Wire rope improvement program. Final report. [For draglines]

Activities in five major areas were undertaken during the WRIP: experiments using PNL-developed bend-over-sheave fatigue test machines to generate data on which to base a model for predicting large-diameter rope performance from that of small-diameter ropes; bend-over-sheave fatigue testing to determine differences in rope failure rates at varying rope loads; analyses to determine how wire ropes actually fail; development of a load sensor to record and quantity operational loads on drag and hoist ropes; and technology transfer activities to disseminate useful program findings to coal mine operators. Data obtained during the 6-year program support are included. High loads on wire ropes are damaging. As an adjunct, however, potentially useful countermeasures to high loads were identified. Large-diameter rope bend-over-sheave performance can be predicted from small-diameter rope test behavior, over some ranges