Dissecting the Gaseous Halos of z~2 Damped Lyα\alpha Systems with Close Quasar Pairs

We use spectroscopy of close pairs of quasars to study diffuse gas in the circumgalactic medium (CGM) surrounding a sample of 40 Damped Lya systems (DLAs). The primary sightline in each quasar pair probes an intervening DLA in the redshift range 1.6 < z_DLA < 3.6, such that the second quasar sightline then probes Lya, CII, SiII, and CIV absorption in the CGM transverse to the DLA to projected distances $R_{\perp} < 300$ kpc. Analysis of the Lya profiles in these CGM sightlines constrains the covering fraction (f_C) of optically thick HI (having column density N_HI > 10^17.2 cm^-2) to be greater than ~30% within $R_{\perp} < 200$ kpc of DLAs. Strong SiII 1526 absorption with equivalent width W_1526 > 0.2 Ang occurs with an incidence f_C (W_1526 > 0.2 Ang) = 20(+12/-8)% within $R_{\perp}<100$ kpc, indicating that low-ionization metal absorption associated with DLAs probes material at a physical distance R_3D < 30 kpc. However, we find that strong CIV 1548 absorption is ubiquitous in these environments (f_C (W_1548 > 0.2 Ang) = 57(+12/-13)% within $R_{\perp} < 100$ kpc), and in addition exhibits a high degree of kinematic coherence on scales up to ~175 kpc. We infer that this high-ionization material arises predominantly in large, quiescent structures extending beyond the scale of the DLA host dark matter halos rather than in ongoing galactic winds. The Lya equivalent width in the DLA-CGM is anticorrelated with $R_{\perp}$ at >98% confidence, suggesting that DLAs arise close to the centers of their host halos rather than on their outskirts. Finally, the average Lya, CII and CIV equivalent widths are consistent with those measured around z~2 Lyman Break Galaxies. Assuming that DLAs trace a galaxy population with lower masses and luminosities, this finding implies that the absorption strength of cool circumgalactic material has a weak dependence on dark matter halo mass for M_h < 10^12 M_sun.Comment: Submitted to ApJ. 30 pages, 13 figures, 3 tables, 1 appendix. Uses emulateapj forma

Stromal cells from the adipose tissue-derived stromal vascular fraction and culture expanded adipose tissue-derived stromal/stem cells: A joint statement of the International Federation for Adipose Therapeutics and Science (IFATS) and the International Society for Cellular Therapy (ISCT)

Adipose tissue is a rich and very convenient source of cells for regenerative medicine therapeutic approaches. However, a characterization of the population of adipose-derived stromal and stem cells (ASCs) with the greatest therapeutic potential remains unclear. Under the authority of International Federation of Adipose Therapeutics and International Society for Cellular Therapy, this paper sets out to establish minimal definitions of stromal cells both as uncultured stromal vascular fraction (SVF) and as an adherent stromal/stem cells population.Phenotypic and functional criteria for the identification of adipose-derived cells were drawn from the literature.In the SVF, cells are identified phenotypically by the following markers: CD45-CD235a-CD31-CD34+. Added value may be provided by both a viability marker and the following surface antigens: CD13, CD73, CD90 and CD105. The fibroblastoid colony-forming unit assay permits the evaluation of progenitor frequency in the SVF population. In culture, ASCs retain markers in common with other mesenchymal stromal/stem cells (MSCs), including CD90, CD73, CD105, and CD44 and remain negative for CD45 and CD31. They can be distinguished from bone-marrow-derived MSCs by their positivity for CD36 and negativity for CD106. The CFU-F assay is recommended to calculate population doublings capacity of ASCs. The adipocytic, chondroblastic and osteoblastic differentiation assays serve to complete the cell identification and potency assessment in conjunction with a quantitative evaluation of the differentiation either biochemically or by reverse transcription polymerase chain reaction.The goal of this paper is to provide initial guidance for the scientific community working with adipose-derived cells and to facilitate development of international standards based on reproducible parameters.Background aims: Adipose tissue is a rich and very convenient source of cells for regenerative medicine therapeutic approaches. However, a characterization of the population of adipose-derived stromal and stem cells (ASCs) with the greatest therapeutic potential remains unclear. Under the authority of International Federation of Adipose Therapeutics and International Society for Cellular Therapy, this paper sets out to establish minimal definitions of stromal cells both as uncultured stromal vascular fraction (SVF) and as an adherent stromal/stem cells population. Methods: Phenotypic and functional criteria for the identification of adipose-derived cells were drawn from the literature. Results: In the SVF, cells are identified phenotypically by the following markers: CD45-CD235a-CD31-CD34+. Added value may be provided by both a viability marker and the following surface antigens: CD13, CD73, CD90 and CD105. The fibroblastoid colony-forming unit assay permits the evaluation of progenitor frequency in the SVF population. In culture, ASCs retain markers in common with other mesenchymal stromal/stem cells (MSCs), including CD90, CD73, CD105, and CD44 and remain negative for CD45 and CD31. They can be distinguished from bone-marrow-derived MSCs by their positivity for CD36 and negativity for CD106. The CFU-F assay is recommended to calculate population doublings capacity of ASCs. The adipocytic, chondroblastic and osteoblastic differentiation assays serve to complete the cell identification and potency assessment in conjunction with a quantitative evaluation of the differentiation either biochemically or by reverse transcription polymerase chain reaction. Conclusions: The goal of this paper is to provide initial guidance for the scientific community working with adipose-derived cells and to facilitate development of international standards based on reproducible parameters. \ua9 2013, International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved

Transcript-indexed ATAC-seq for precision immune profiling.

T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of&nbsp;cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy

On the fourth-order accurate compact ADI scheme for solving the unsteady Nonlinear Coupled Burgers' Equations

The two-dimensional unsteady coupled Burgers' equations with moderate to severe gradients, are solved numerically using higher-order accurate finite difference schemes; namely the fourth-order accurate compact ADI scheme, and the fourth-order accurate Du Fort Frankel scheme. The question of numerical stability and convergence are presented. Comparisons are made between the present schemes in terms of accuracy and computational efficiency for solving problems with severe internal and boundary gradients. The present study shows that the fourth-order compact ADI scheme is stable and efficient

The SWELLS Survey. I. A large spectroscopically selected sample of edge-on late-type lens galaxies

The relative contribution of baryons and dark matter to the inner regions of spiral galaxies provides critical clues to their formation and evolution, but it is generally difficult to determine. For spiral galaxies that are strong gravitational lenses, however, the combination of lensing and kinematic observations can be used to break the disk-halo degeneracy. In turn, such data constrain fundamental parameters such as i) the mass density profile slope and axis ratio of the dark matter halo, and by comparison with dark matter-only numerical simulations the modifications imposed by baryons; ii) the mass in stars and therefore the overall star formation efficiency, and the amount of feedback; iii) by comparison with stellar population synthesis models, the normalization of the stellar initial mass function. In this first paper of a series, we present a sample of 16 secure, 1 probable, and 6 possible strong lensing spiral galaxies, for which multi-band high-resolution images and rotation curves were obtained using the Hubble Space Telescope and Keck-II Telescope as part of the Sloan WFC Edge-on Late-type Lens Survey (SWELLS). The sample includes 8 newly discovered secure systems. [abridged] We find that the SWELLS sample of secure lenses spans a broad range of morphologies (from lenticular to late-type spiral), spectral types (quantified by Halpha emission), and bulge to total stellar mass ratio (0.22-0.85), while being limited to M_*>10^{10.5} M_sun. The SWELLS sample is thus well-suited for exploring the relationship between dark and luminous matter in a broad range of galaxies. We find that the deflector galaxies obey the same size-mass relation as that of a comparison sample of elongated non-lens galaxies selected from the SDSS survey. We conclude that the SWELLS sample is consistent with being representative of the overall population of high-mass high-inclination disky galaxies.Comment: 21 pages, 6 figures, MNRAS, in pres

Functional network disorganization and cognitive decline following fractionated whole-brain radiation in mice

Cognitive dysfunction following radiotherapy (RT) is one of the most common complications associated with RT delivered to the brain, but the precise mechanisms behind this dysfunction are not well understood, and to date, there are no preventative measures or effective treatments. To improve patient outcomes, a better understanding of the effects of radiation on the brain\u27s functional systems is required. Functional magnetic resonance imaging (fMRI) has shown promise in this regard, however, compared to neural activity, hemodynamic measures of brain function are slow and indirect. Understanding how RT acutely and chronically affects functional brain organization requires more direct examination of temporally evolving neural dynamics as they relate to cerebral hemodynamics for bridging with human studies. In order to adequately study the underlying mechanisms of RT-induced cognitive dysfunction, the development of clinically mimetic RT protocols in animal models is needed. To address these challenges, we developed a fractionated whole-brain RT protocol (3Gy/day for 10 days) and applied longitudinal wide field optical imaging (WFOI) of neural and hemodynamic brain activity at 1, 2, and 3 months post RT. At each time point, mice were subject to repeated behavioral testing across a variety of sensorimotor and cognitive domains. Disruptions in cortical neuronal and hemodynamic activity observed 1 month post RT were significantly worsened by 3 months. While broad changes were observed in functional brain organization post RT, brain regions most impacted by RT occurred within those overlapping with the mouse default mode network and other association areas similar to prior reports in human subjects. Further, significant cognitive deficits were observed following tests of novel object investigation and responses to auditory and contextual cues after fear conditioning. Our results fill a much-needed gap in understanding the effects of whole-brain RT on systems level brain organization and how RT affects neuronal versus hemodynamic signaling in the cortex. Having established a clinically-relevant injury model, future studies can examine therapeutic interventions designed to reduce neuroinflammation-based injury following RT. Given the overlap of sequelae that occur following RT with and without chemotherapy, these tools can also be easily incorporated to examine chemotherapy-related cognitive impairment

Quasars Probing Quasars. VI. Excess H I Absorption within one Proper Mpc of z ~ 2 Quasars

With close pairs of quasars at different redshifts, a background quasar sightline can be used to study a foreground quasar's environment in absorption. We use a sample of 650 projected quasar pairs to study the H I Lyα absorption transverse to luminous, z ~ 2 quasars at proper separations of 30 kpc 10^(17.3) cm^(-2) at separations R_⊥ < 200 kpc, which decreases to ~20% at R_⊥ ≃ 1 Mpc, but still represents a significant excess over the cosmic average. This excess of optically thick absorption can be described by a quasar-absorber cross-correlation function ξ_(QA)(r) = (r/r_0)^γ with a large correlation length r_0=12.5^(+2.7)_(-1.4)h^(-1)Mpc(comoving) and y =1.68^(+0.14)_(-0.30). The H I absorption measured around quasars exceeds that of any previously studied population, consistent with quasars being hosted by massive dark matter halos M_(halo) ≈ 10^(12.5) M_☉ at z ~ 2.5. The environments of these massive halos are highly biased toward producing optically thick gas, and may even dominate the cosmic abundance of Lyman limit systems and hence the intergalactic opacity to ionizing photons at z ~ 2.5. The anisotropic absorption around quasars implies the transverse direction is much less likely to be illuminated by ionizing radiation than the line-of-sight