Histone deacetylases in replicative senescence: evidence for a senescence-specific form of HDAC-2

AbstractTo analyze mechanisms of senescence-associated gene expression, we have investigated histone deacetylases (HDACs) in human fibroblasts undergoing replicative senescence. We found that the overall acetylation pattern of histones does not vary detectably with replicative senescence. By Northern blot and Western blot, we found a significant decrease in the abundance of HDAC-1 in senescent cells. Biochemical analysis of deacetylase activities in extracts from old and young cells revealed a striking difference. While by anion exchange chromatography we found a single peak of activity in extracts from young cells, which coincided with the elution of both HDAC-1 and HDAC-2, in senescent cells a second peak of activity was found. This second peak of activity is associated with HDAC-2 but does not contain HDAC-1. These results suggest that HDAC-2 is present in at least two distinct forms, one of which is specific for senescent cells. Further biochemical characterization of the enzyme activity revealed that addition of nicotinamide adenine dinucleotide (NAD) did not detectably influence the activity of any fraction, suggesting that NAD is not an essential co-factor for the analyzed HDACs from diploid human fibroblasts

Star Formation in Sculptor Group Dwarf Irregular Galaxies and the Nature of "Transition" Galaxies

We present new H-alpha narrow band imaging of the HII regions in eight Sculptor Group dwarf irregular (dI) galaxies. Comparing the Sculptor Group dIs to the Local Group dIs, we find that the Sculptor Group dIs have, on average, lower values of SFR when normalized to either galaxy luminosity or gas mass (although there is considerable overlap between the two samples). The properties of ``transition'' (dSph/dIrr) galaxies in Sculptor and the Local Group are also compared and found to be similar. The transition galaxies are typically among the lowest luminosities of the gas rich dwarf galaxies. Relative to the dwarf irregular galaxies, the transition galaxies are found preferentially nearer to spiral galaxies, and are found nearer to the center of the mass distribution in the local cloud. While most of these systems are consistent with normal dI galaxies which currently exhibit temporarily interrupted star formation, the observed density-morphology relationship (which is weaker than that observed for the dwarf spheroidal galaxies) indicates that environmental processes such as ``tidal stirring'' may play a role in causing their lower SFRs.Comment: 35 pages, 10 figures, accepted for Feb 2003 AJ, companion to astro-ph/021117

On the Structural Differences between Disk and Dwarf Galaxies

Gas-rich dwarf and disk galaxies overlap in numerous physical quantities that make their classification subjective. We report the discovery of a separation between dwarfs and disks into two unique sequences in the mass (luminosity) versus scale length plane. This provides an objective classification scheme for late-type galaxies that only requires optical or near-IR surface photometry of a galaxy. Since the baryonic Tully-Fisher relation for these samples produces a continuous relation between baryonic mass and rotational velocity, we conclude that the difference between dwarfs and disks must be because of their distribution of stellar light such that dwarfs are more diffuse than disk galaxies. This structural separation may be due to a primordial difference between low and high mass galaxies or produced by hierarchical mergers where disks are built up from dwarfs. Structural differences between dwarf and disk galaxies may also be driven by the underlying kinematics where the strong rotation in disks produces an axial symmetric object that undergoes highly efficient star formation in contrast to the lower rotation, more disordered motion of dwarfs that produces a diffuse, triaxial object with a history of inefficient star formation.Comment: 16 pages, 2 figures, AJ in press, AASTeX5.

Stromgren Photometry from z=0 to z~1. The Method

We use rest-frame Stromgren photometry to observe clusters of galaxies in a self-consistent manner from z=0 to z=0.8. Stromgren photometry of galaxies is an efficient compromise between standard broad-band photometry and spectroscopy, in the sense that it is more sensitive to subtle variations in spectral energy distributions than the former, yet much less time-consuming than the latter. Principal Component Analysis (PCA) is used to extract maximum information from the Stromgren data. By calibrating the Principal Components using well-studied galaxies (and stellar population models), we develop a purely empirical method to detect, and subsequently classify, cluster galaxies at all redshifts smaller than 0.8. Interlopers are discarded with unprecedented efficiency (up to 100%). The first Principal Component essentially reproduces the Hubble Sequence, and can thus be used to determine the global star formation history of cluster members. The (PC2, PC3) plane allows us to identify Seyfert galaxies (and distinguish them from starbursts) based on photometric colors alone. In the case of E/S0 galaxies with known redshift, we are able to resolve the age-dust- metallicity degeneracy, albeit at the accuracy limit of our present observations. This technique will allow us to probe galaxy clusters well beyond their cores and to fainter magnitudes than spectroscopy can achieve. We are able to directly compare these data over the entire redshift range without a priori assumptions because our observations do not require k-corrections. The compilation of such data for different cluster types over a wide redshift range is likely to set important constraints on the evolution of galaxies and on the clustering process.Comment: 35 pages, 18 figures, accepted by ApJ

Tversky loss function for image segmentation using 3D fully convolutional deep networks

Fully convolutional deep neural networks carry out excellent potential for fast and accurate image segmentation. One of the main challenges in training these networks is data imbalance, which is particularly problematic in medical imaging applications such as lesion segmentation where the number of lesion voxels is often much lower than the number of non-lesion voxels. Training with unbalanced data can lead to predictions that are severely biased towards high precision but low recall (sensitivity), which is undesired especially in medical applications where false negatives are much less tolerable than false positives. Several methods have been proposed to deal with this problem including balanced sampling, two step training, sample re-weighting, and similarity loss functions. In this paper, we propose a generalized loss function based on the Tversky index to address the issue of data imbalance and achieve much better trade-off between precision and recall in training 3D fully convolutional deep neural networks. Experimental results in multiple sclerosis lesion segmentation on magnetic resonance images show improved F2 score, Dice coefficient, and the area under the precision-recall curve in test data. Based on these results we suggest Tversky loss function as a generalized framework to effectively train deep neural networks

On the Nature of Soft X-ray Weak Quasi-Stellar Objects

Recent studies of QSOs with ROSAT suggest the existence of a significant population of Soft X-ray Weak QSOs (SXW QSOs) where the soft X-ray flux is ~ 10-30 times smaller than in typical QSOs. As a first step in a systematic study of these objects, we establish a well-defined sample of SXW QSOs which includes all alpha_ox<=-2 QSOs from the Boroson & Green (1992) sample of 87 BQS QSOs. SXW QSOs comprise about 11% of this optically selected QSO sample. From an analysis of CIV absorption in the 55 BG92 QSOs with available CIV data, we find a remarkably strong correlation between alpha_ox and the CIV absorption equivalent width. This correlation suggests that absorption is the primary cause of soft X-ray weakness in QSOs, and it reveals a continuum of absorption properties connecting unabsorbed QSOs, X-ray warm absorber QSOs, SXW QSOs and BAL QSOs. From a practical point of view, our correlation demonstrates that selection by soft X-ray weakness is an effective (>=80% successful) and observationally inexpensive way to find low-redshift QSOs with strong and interesting ultraviolet absorption. We have also identified several notable differences between the optical emission-line properties of SXW QSOs and those of the other BG92 QSOs. SXW QSOs show systematically low [O III] luminosities as well as distinctive H-beta profiles. They tend to lie toward the weak-[O III] end of BG92 eigenvector 1, as do many low-ionization BAL QSOs. Unabsorbed Seyferts and QSOs with similar values of eigenvector 1 have been suggested to have extreme values of a primary physical parameter, perhaps mass accretion rate relative to the Eddington rate (M-dot/M-dot_{Edd}). If these suggestions are correct, it is likely that SXW QSOs also tend to have generally high values of (M-dot/M-dot_{Edd}). (Abridged)Comment: 34 pages, ApJ accepted, also available from http://www.astro.psu.edu/users/niel/papers/papers.htm

Modeling of the Super-Eddington Phase for Classical Novae: Five IUE Novae

We present a light curve model for the super-Eddington luminosity phase of five classical novae observed with IUE. Optical and UV light curves are calculated based on the optically thick wind theory with a reduced effective opacity for a porous atmosphere. Fitting a model light curve with the UV 1455 \AA light curve, we determine the white dwarf mass and distance to be (1.3 M_sun, 4.4 kpc) for V693 CrA, (1.05 M_sun, 1.8 kpc) for V1974 Cyg, (0.95 M_sun, 4.1 kpc) for V1668 Cyg, (1.0 M_sun, 2.1 kpc) for V351 Pup, and (1.0 M_sun, 4.3 kpc) for OS And.Comment: 9 pages including 8 figures, to appear in the Astrophysical Journa

WSO/UV: World Space Observatory/Ultraviolet

We summarize the capabilities of the World Space Observatory (UV) Project (WSO/UV). An example of the importance of this project (with a planned launch date of 2007/8) for the study of Classical Novae is given.Comment: 4 pages, To appear in the proceeedings of the "Classical Nova Explosions" conference, eds. M. Hernanz and J. Jose, AI

Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the Metabolism of the Adult Liver in Mice and Human

The Hedgehog (Hh) and Wnt/β-Catenin (Wnt) cascades are morphogen pathways whose pronounced influence on adult liver metabolism has been identified in recent years. How both pathways communicate and control liver metabolic functions are largely unknown. Detecting core components of Wnt and Hh signaling and mathematical modeling showed that both pathways in healthy liver act largely complementary to each other in the pericentral (Wnt) and the periportal zone (Hh) and communicate mainly by mutual repression. The Wnt/Hh module inversely controls the spatiotemporal operation of various liver metabolic pathways, as revealed by transcriptome, proteome, and metabolome analyses. Shifting the balance to Wnt (activation) or Hh (inhibition) causes pericentralization and periportalization of liver functions, respectively. Thus, homeostasis of the Wnt/Hh module is essential for maintaining proper liver metabolism and to avoid the development of certain metabolic diseases. With caution due to minor species-specific differences, these conclusions may hold for human liver as well