The Long-Term Variability of the X-Ray Sources in NGC 6946 and NGC 4485/4490

We analyze data from five Chandra observations of the spiral galaxy NGC 6946 and from three Chandra observations of the irregular/spiral interacting galaxy pair NGC 4485/4490, with an emphasis on investigating the long-term variability exhibited by the source populations. We detect 90 point sources coincident with NGC 6946 down to luminosities of a few times 10^36 erg/s, and 38 sources coincident with NGC 4485/90 down to a luminosity of ~1x10^37 erg/s. Twenty-five (15) sources in NGC 6946 (NGC 4485/90) exhibit long-term (i.e., weeks to years) variability in luminosity; 11 (4) are transient candidates. The single ultraluminous X-ray source (ULX) in NGC 6946 and all but one of the eight ULXs in NGC 4485/90 exhibit long-term flux variability. Two of the ULXs in NGC 4485/90 have not been identified before as ultraluminous sources. The widespread variability in both systems is indicative of the populations being dominated by X-ray binaries, and this is supported by the X-ray colors of the sources. The distribution of colors among the sources indicates a large fraction of high-mass X-ray binaries in both systems. The shapes of the X-ray luminosity functions of the galaxies do not change significantly between observations and can be described by power laws with cumulative slopes ~0.6-0.7 (NGC 6946) and ~0.4 (NGC 4485/90).Comment: 26 pages, 9 figures, 15 tables - to appear in the August 2008 issue of ApJS - new version corrects a few typo

Network Archaeology: Uncovering Ancient Networks from Present-day Interactions

Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these limitations, we propose several algorithms for reconstructing a network's history of growth given only the network as it exists today and a generative model by which the network is believed to have evolved. Our likelihood-based method finds a probable previous state of the network by reversing the forward growth model. This approach retains node identities so that the history of individual nodes can be tracked. We apply these algorithms to uncover older, non-extant biological and social networks believed to have grown via several models, including duplication-mutation with complementarity, forest fire, and preferential attachment. Through experiments on both synthetic and real-world data, we find that our algorithms can estimate node arrival times, identify anchor nodes from which new nodes copy links, and can reveal significant features of networks that have long since disappeared.Comment: 16 pages, 10 figure

Paradoxical patterns of sinusoidal obstruction syndrome-like liver injury in aged female CD-1 mice triggered by cannabidiol-rich cannabis extract and acetaminophen co-administration

© 2019 The Authors. Environmental Toxicology published by Wiley Periodicals, Inc. Exposure to environmental contaminants and consumption of a high, saturated fatty diet has been demonstrated to promote precursors for metabolic syndrome (hyperglycemia, hyperinsulinemia, and hypertriglyceridemia). The purpose of this study was to determine if exposure to the most prevalent environmental persistent organic pollutants (POPs) would act as causative agents to promote metabolic syndrome independent of dietary intake. We hypothesized that POPs will activate the advanced glycated end-product (AGE)-and receptor for AGE (RAGE) signaling cascade to promote downstream signaling modulators of cardiovascular remodeling and oxidative stress in the heart. At 5-weeks of age nondiabetic (WT) and diabetic (ob/ob) mice were exposed POPs mixtures by oral gavage twice a week for 6-weeks. At the end of 6-weeks, animals were sacrificed and the hearts were taken for biochemical analysis. Increased activation of the AGE-RAGE signaling cascade via POPs exposure resulted in elevated levels of fibroblast differentiation (α-smooth muscle actin) and RAGE expression indicated maladaptive cardiac remodeling. Conversely, the observed decreased superoxide dismutase-1 and -2 (SOD-1 and SOD-2) expression may exacerbate the adverse changes occurring as a result of POPs treatment to reduce innate cardioprotective mechanisms. In comparison, ventricular collagen levels were decreased in mice exposed to POPs. In conclusion, exposure to organic environmental pollutants may intensify oxidative and inflammatory stressors to overwhelm protective mechanisms allowing for adverse cardiac remodeling

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected

Large-scale clustering of Lyman \u3b1 emission intensity from SDSS/BOSS

We present a tentative detection of the large-scale structure of Ly \u3b1 emission in the Universe at redshifts z = 2-3.5 by measuring the cross-correlation of Ly \u3b1 surface brightness with quasars in Sloan Digital Sky Survey/Baryon Oscillation Spectroscopic Survey.We use amillion spectra targeting luminous red galaxies at z < 0.8, after subtracting a best-fitting model galaxy spectrum from each one, as an estimate of the high-redshift Ly \u3b1 surface brightness. The quasar- Ly \u3b1 emission cross-correlation is detected on scales 1 ~ 15 h-1 Mpc, with shape consistent with a \u39b (CDM model with) \u3a9m = 0.30+0.10 -0.07. The predicted amplitude of this cross-correlation is proportional to the product of the mean Ly \u3b1 surface brightness, (\u3bc\u3b1), the amplitude of mass fluctuations and the quasar and Ly \u3b1 emission bias factors. We infer (\u3bc\u3b1) (b\u3b1/3) = (3.9 \ub1 0.9) 7 10-21 erg s-1 cm-2 \uc5-1 arcsec-2, where b\u3b1 is the Ly \u3b1 emission bias. If star-forming galaxies dominate this emission, we find \u3c1SFR = (0.28 \ub1 0.07)(3/b\u3b1) yr-1 Mpc-3. For b\u3b1 = 3, this value is~30 times larger than previous estimates from individually detected Ly \u3b1 emitters, but consistent with the total \u3c1SFR derived from dust-corrected, continuum UV galaxy surveys, if most of the Ly \u3b1 photons from these galaxies avoid dust absorption and are reemitted after diffusing in large gas haloes. Heating of intergalactic gas by He II photoionization from quasar radiation or jets may alternatively explain the detected correlation, and cooling radiation from gas in galactic haloes may also contribute. We also detect redshift space anisotropy of the quasar-Ly \u3b1 emission cross-correlation, finding evidence at the 3.0\u3c3 level that it is radially elongated, which may be explained by radiative-transfer effects. Our measurements represent the first application of the intensity mapping technique to optical observations. \ua9 2016 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society

The Impact of Multifunctional Genes on "Guilt by Association" Analysis

Many previous studies have shown that by using variants of “guilt-by-association”, gene function predictions can be made with very high statistical confidence. In these studies, it is assumed that the “associations” in the data (e.g., protein interaction partners) of a gene are necessary in establishing “guilt”. In this paper we show that multifunctionality, rather than association, is a primary driver of gene function prediction. We first show that knowledge of the degree of multifunctionality alone can produce astonishingly strong performance when used as a predictor of gene function. We then demonstrate how multifunctionality is encoded in gene interaction data (such as protein interactions and coexpression networks) and how this can feed forward into gene function prediction algorithms. We find that high-quality gene function predictions can be made using data that possesses no information on which gene interacts with which. By examining a wide range of networks from mouse, human and yeast, as well as multiple prediction methods and evaluation metrics, we provide evidence that this problem is pervasive and does not reflect the failings of any particular algorithm or data type. We propose computational controls that can be used to provide more meaningful control when estimating gene function prediction performance. We suggest that this source of bias due to multifunctionality is important to control for, with widespread implications for the interpretation of genomics studies

Standards in semen examination:publishing reproducible and reliable data based on high-quality methodology

Biomedical science is rapidly developing in terms of more transparency, openness and reproducibility of scientific publications. This is even more important for all studies that are based on results from basic semen examination. Recently two concordant documents have been published: the 6th edition of the WHO Laboratory Manual for the Examination and Processing of Human Semen, and the International Standard ISO 23162:2021. With these tools, we propose that authors should be instructed to follow these laboratory methods in order to publish studies in peer-reviewed journals, preferable by using a checklist as suggested in an Appendix to this article.Peer reviewe

The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: cosmological analysis of the DR12 galaxy sample

We present cosmological results from the final galaxy clustering data set of the Baryon Oscillation Spectroscopic Survey, part of the Sloan Digital Sky Survey III. Our combined galaxy sample comprises 1.2 million massive galaxies over an effective area of 9329 $deg^2$ and volume of 18.7 $Gpc^3$, divided into three partially overlapping redshift slices centred at effective redshifts 0.38, 0.51, and 0.61. We measure the angular diameter distance DM and Hubble parameter H from the baryon acoustic oscillation (BAO) method after applying reconstruction to reduce non-linear effects on the BAO feature. Using the anisotropic clustering of the pre-reconstruction density field, we measure the product DM*H from the Alcock-Paczynski (AP) effect and the growth of structure, quantified by $f{\sigma}8(z)$, from redshift-space distortions (RSD). We combine measurements presented in seven companion papers into a set of consensus values and likelihoods, obtaining constraints that are tighter and more robust than those from any one method. Combined with Planck 2015 cosmic microwave background measurements, our distance scale measurements simultaneously imply curvature ${\Omega}_K =0.0003+/-0.0026$ and a dark energy equation of state parameter w = -1.01+/-0.06, in strong affirmation of the spatially flat cold dark matter model with a cosmological constant (${\Lambda}$CDM). Our RSD measurements of $f{\sigma}_8$, at 6 per cent precision, are similarly consistent with this model. When combined with supernova Ia data, we find H0 = 67.3+/-1.0 km/s/Mpc even for our most general dark energy model, in tension with some direct measurements. Adding extra relativistic species as a degree of freedom loosens the constraint only slightly, to H0 = 67.8+/-1.2 km/s/Mpc. Assuming flat ${\Lambda}$CDM we find ${\Omega}_m = 0.310+/-0.005$ and H0 = 67.6+/-0.5 km/s/Mpc, and we find a 95% upper limit of $0.16 eV/c^2$ on the neutrino mass sum

Cosmological implications of baryon acoustic oscillation measurements

We derive constraints on cosmological parameters and tests of dark energy models from the combination of baryon acoustic oscillation (BAO) measurements with cosmic microwave background (CMB) data and a recent reanalysis of Type Ia supernova (SN) data. In particular, we take advantage of high-precision BAO measurements from galaxy clustering and the Lyman-α forest (LyaF) in the SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS). Treating the BAO scale as an uncalibrated standard ruler, BAO data alone yield a high confidence detection of dark energy; in combination with the CMB angular acoustic scale they further imply a nearly flat universe. Adding the CMB-calibrated physical scale of the sound horizon, the combination of BAO and SN data into an “inverse distance ladder” yields a measurement of H0 =67.3 ± 1.1 km s-1 Mpc-1, with 1.7% precision. This measurement assumes standard prerecombination physics but is insensitive to assumptions about dark energy or space curvature, so agreement with CMB-based estimates that assume a flat Λ CDM cosmology is an important corroboration of this minimal cosmological model. For constant dark energy (Λ), our BAO + SN + CMB combination yields matter density Ωm = 0.301 ± 0.008 and curvature Ωk = -0.003 ± 0.003. When we allow more general forms of evolving dark energy, the BAO + SN + CMB parameter constraints are always consistent with flat Λ CDM values at ≈1σ. While the overall χ2 of model fits is satisfactory, the LyaF BAO measurements are in moderate (2–2.5σ) tension with model predictions. Models with early dark energy that tracks the dominant energy component at high redshift remain consistent with our expansion history constraints, and they yield a higher H0 and lower matter clustering amplitude, improving agreement with some low redshift observations. Expansion history alone yields an upper limit on the summed mass of neutrino species, ∑mν (95% confidence), improving to ∑mν if we include the lensing signal in the Planck CMB power spectrum. In a flat Λ CDM model that allows extra relativistic species, our data combination yields Neff = 3.43 ± 0.26; while the LyaF BAO data prefer higher Neff when excluding galaxy BAO, the galaxy BAO alone favor Neff ≈ 3. When structure growth is extrapolated forward from the CMB to low redshift, standard dark energy models constrained by our data predict a level of matter clustering that is high compared to most, but not all, observational estimates

Global economic burden of unmet surgical need for appendicitis

Background: There is a substantial gap in provision of adequate surgical care in many low-and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods: Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results: Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion: For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially