A Comparison of Circumgalactic Mg ii Absorption between the TNG50 Simulation and the MEGAFLOW Survey

The circumgalactic medium (CGM) contains information on gas flows around galaxies, such as accretion and supernova-driven winds, which are difficult to constrain from observations alone. Here, we use the high-resolution TNG50 cosmological magnetohydrodynamical simulation to study the properties and kinematics of the CGM around star-forming galaxies in 1011.5-1012 M o˙ halos at z ≃ 1 using mock Mg ii absorption lines, which we generate by postprocessing halos to account for photoionization in the presence of a UV background. We find that the Mg ii gas is a very good tracer of the cold CGM, which is accreting inward at inflow velocities of up to 50 km s-1. For sight lines aligned with the galaxy's major axis, we find that Mg ii absorption lines are kinematically shifted due to the cold CGM's significant corotation at speeds up to 50% of the virial velocity for impact parameters up to 60 kpc. We compare mock Mg ii spectra to observations from the MusE GAs FLow and Wind (MEGAFLOW) survey of strong Mg ii absorbers (EW2796 Å0 > 0.5 Å). After matching the equivalent-width (EW) selection, we find that the mock Mg ii spectra reflect the diversity of observed kinematics and EWs from MEGAFLOW, even though the sight lines probe a very small fraction of the CGM. Mg ii absorption in higher-mass halos is stronger and broader than in lower-mass halos but has qualitatively similar kinematics. The median-specific angular momentum of the Mg ii CGM gas in TNG50 is very similar to that of the entire CGM and only differs from non-CGM components of the halo by normalization factors of ≲1 dex

Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview

Thanks to innovative sample-preparation and sequencing technologies, gene expression in individual cells can now be measured for thousands of cells in a single experiment. Since its introduction, single-cell RNA sequencing (scRNA-seq) approaches have revolutionized the genomics field as they created unprecedented opportunities for resolving cell heterogeneity by exploring gene expression profiles at a single-cell resolution. However, the rapidly evolving field of scRNA-seq invoked the emergence of various analytics approaches aimed to maximize the full potential of this novel strategy. Unlike population-based RNA sequencing approaches, scRNA seq necessitates comprehensive computational tools to address high data complexity and keep up with the emerging single-cell associated challenges. Despite the vast number of analytical methods, a universal standardization is lacking. While this reflects the fields’ immaturity, it may also encumber a newcomer to blend in. In this review, we aim to bridge over the abovementioned hurdle and propose four ready-to-use pipelines for scRNA-seq analysis easily accessible by a newcomer, that could fit various biological data types. Here we provide an overview of the currently available single-cell technologies for cell isolation and library preparation and a step by step guide that covers the entire canonical analytic workflow to analyse scRNA-seq data including read mapping, quality controls, gene expression quantification, normalization, feature selection, dimensionality reduction, and cell clustering useful for trajectory inference and differential expression. Such workflow guidelines will escort novices as well as expert users in the analysis of complex scRNA-seq datasets, thus further expanding the research potential of single-cell approaches in basic science, and envisaging its future implementation as best practice in the field

Rapid activation and down-regulation of protein kinase C alpha in 12-O-tetradecanoylphorbol-13-acetate -induced differentiation of human rhabdomyosarcoma cells

Human rhabdomyosarcoma RD cells express the myogenic regulatory factors MyoD and myogenin but differentiate spontaneously very poorly. Prolonged treatment of RD cells with the protein kinase C (PKC) activator 12-O-tetradecanoylphorbol-13-acetate (TPA) induces growth arrest and myogenic differentiation as shown by the accumulation of alpha-actin and myosin light and heavy chains, without affecting the expression of MyoD and myogenin. In this study, we show that short-term phorbol ester treatment of the cultures is sufficient to trigger myogenic differentiation but not growth arrest. Furthermore, PKC inhibitors, such as staurosporine or calphostin C, prevent TPA-induced differentiation but not cell growth arrest. These data suggest that the two events are mediated by different pathways; a possible interpretation is that the activation of one or more PKC isoforms mediates the induction of differentiation, whereas the down-regulation of the same or different isoforms mediates the growth arrest. To address the mechanism whereby TPA affects cell growth and differentiation in RD cells, we first analyzed PKC isoenzyme distribution. We found that RD cells express the alpha, beta 1, gamma, and sigma PKC isoenzymes. Only the alpha isoform is exclusively found in the soluble fraction, but it translocates to the membrane fraction within 5 min of TPA treatment and is completely down-regulated after 6 h. The other isoenzymes are found associated to both the soluble and the particulate fractions and are down-regulated after long-term TPA treatment. By immunofluorescence analysis, we show that the PKC alpha down-regulation is specific for those cells that respond to TPA by activating the muscle phenotype. We propose that TPA-induced differentiation in RD cells is mediated by the transient activation of PKC alpha, which activates some of the intracellular events that are necessary for MyoD and myogenin transacting activity and for the induction of terminal differentiation of RD cells. By contrast, the constitutively active beta 1 and sigma are responsible for the maintenance of cell growth, and their down-regulation is responsible for long-term TPA-induced cell growth arrest

The Blue Straggler population in the globular cluster M53 (NGC5024): a combined HST, LBT, CFHT study

We used a proper combination of multiband high-resolution and wide field multi-wavelength observations collected at three different telescopes (HST, LBT and CFHT) to probe Blue Straggler Star (BSS) populations in the globular cluster M53. Almost 200 BSS have been identified over the entire cluster extension. The radial distribution of these stars has been found to be bimodal (similarly to that of several other clusters) with a prominent dip at ~60'' (~2 r_c) from the cluster center. This value turns out to be a factor of two smaller than the radius of avoidance (r_avoid, the radius within which all the stars of ~1.2 M_sun have sunk to the core because of dynamical friction effects in an Hubble time). While in most of the clusters with a bimodal BSS radial distribution, r_avoid has been found to be located in the region of the observed minimum, this is the second case (after NGC6388) where this discrepancy is noted. This evidence suggests that in a few clusters the dynamical friction seems to be somehow less efficient than expected. We have also used this data base to construct the radial star density profile of the cluster: this is the most extended and accurate radial profile ever published for this cluster, including detailed star counts in the very inner region. The star density profile is reproduced by a standard King Model with an extended core (~25'') and a modest value of the concentration parameter (c=1.58). A deviation from the model is noted in the most external region of the cluster (at r>6.5' from the center). This feature needs to be further investigated in order to address the possible presence of a tidal tail in this cluster.Comment: 25 pages, 9 figures, accepted for publication on Ap

SINFONI Integral Field Spectroscopy of z~2 UV-selected Galaxies: Rotation Curves and Dynamical Evolution

We present 0.5" resolution near-IR integral field spectroscopy of the Ha line emission of 14 z~2 UV-selected BM/BX galaxies obtained with SINFONI at ESO/VLT. The mean Ha half-light radius r_1/2 is about 4kpc and line emission is detected over > ~20kpc in several sources. In 9 sources, we detect spatially-resolved velocity gradients, from 40 to 410 km/s over ~10kpc. The observed kinematics of the larger systems are consistent with orbital motions. Four galaxies are well described by rotating disks with clumpy morphologies and we extract rotation curves out to radii > ~10kpc. One or two galaxies exhibit signatures more consistent with mergers. Analyzing all 14 galaxies in the framework of rotating disks, we infer mean inclination- and beam-corrected maximum circular velocities v_c of 180+-90 km/s and dynamical masses of (0.5-25)x10^10 Msun within r_1/2. On average, the dynamical masses are consistent with photometric stellar masses assuming a Chabrier/Kroupa IMF but too small for a 0.1-100 Msun Salpeter IMF. The specific angular momenta of our BM/BX galaxies are similar to those of local late-type galaxies. The specific angular momenta of their baryons are comparable to those of their dark matter halos. Extrapolating from the average v_c at 10kpc, the virial mass of the typical halo of a galaxy in our sample is 10^(11.7+-0.5) Msun. Kinematic modeling of the 3 best cases implies a ratio of v_c to local velocity dispersion of order 2-4 and accordingly a large geometric thickness. We argue that this suggests a mass accretion (alternatively, gas exhaustion) timescale of ~500Myr. We also argue that if our BM/BX galaxies were initially gas rich, their clumpy disks will subsequently lose their angular momentum and form compact bulges on a timescale of ~1 Gyr. [ABRIDGED]Comment: Accepted for publication in the Astrophysical Journal. 17 pages, 5 color figure

The common-866G > A variant in the promoter of UCP2 is associated with decreased risk of coronary artery disease in type 2 diabetic men

OBJECTIVE-Uncoupling protein 2 (UCP2) is a physiological downregulator of reactive oxygen species generation and plays an antiatherogenic role in the vascular wall. A common variant in the UCP2 promoter (-866G>A) modulates mRNA expression, with increased expression associated with the A allele. We investigated association of this variant with coronary artery disease (CAD) in two cohorts of type 2 diabetic subjects.RESEARCH DESIGN and METHODS-We studied 3,122 subjects from the 6-year prospective Non-Insulin-Dependent Diabetes, Hypertension, Microalbuminuria, Cardiovascular Events, and Ramipril (DIABHYCAR) Study (14.9% of CAD incidence at follow-up). An independent, hospital-based cohort of 335 men, 52% of whom had CAD, was also studied.RESULTS-We observed an inverse association of the A allele with incident cases of CAD in a dominant model (hazard risk 0.88 [95% CI 0.80-0.96]; P = 0.006). Similar results were observed for baseline cases of CAD. Stratification by sex confirmed an allelic association with CAD in men, whereas no association was observed in women. All CAD phenotypes considered-myocardial infarction, angina pectoris, coronary artery bypass graft (CABG), and sudden death-contributed significantly to the association. Results were replicated in a cross-sectional study of an independent cohort (odds ratio 0.47 [95% CI 0.25-0.89]; P = 0.02 for a recessive model).CONCLUSIONS-The A allele of the -866G>A variant of UCP2 was associated with reduced risk of CAD in men with type 2 diabetes in a 6-year prospective study. Decreased risk of myocardial infarction, angina pectoris, CABG, and sudden death contributed individually and significantly to the reduction of CAD risk. This association was independent of other common CAD risk factors.INSERM, Fac Med Xavier Bichat, U695, F-75018 Paris, FranceCochin Hosp, AP HP, Dept Immunol & Diabetol, Paris, FranceUniv São Paulo, Lab Cellular & Mol Endocrinol, São Paulo, BrazilUniversidade Federal de São Paulo, Mol Endocrinol Lab, São Paulo, BrazilFed Fac Fdn Med Sci Porto Alegre, Post Grad Program Med Sci, Porto Alegre, RS, BrazilHop La Pitie Salpetriere, Dept Cardiol, AP HP, Paris, FranceUniv Paris 07, Paris, FranceUniv Paris 05, Paris, FranceUniversidade Federal de São Paulo, Mol Endocrinol Lab, São Paulo, BrazilWeb of Scienc

Probabilistic analysis of the upwind scheme for transport

We provide a probabilistic analysis of the upwind scheme for multi-dimensional transport equations. We associate a Markov chain with the numerical scheme and then obtain a backward representation formula of Kolmogorov type for the numerical solution. We then understand that the error induced by the scheme is governed by the fluctuations of the Markov chain around the characteristics of the flow. We show, in various situations, that the fluctuations are of diffusive type. As a by-product, we prove that the scheme is of order 1/2 for an initial datum in BV and of order 1/2-a, for all a>0, for a Lipschitz continuous initial datum. Our analysis provides a new interpretation of the numerical diffusion phenomenon

Non variability of intervening absorbers observed in the UVES spectra of the "naked-eye" GRB080319

The aim of this paper is to investigate the properties of the intervening absorbers lying along the line of sight of Gamma-Ray Burst (GRB) 080319B through the analysis of its optical absorption features. To this purpose, we analyze a multi-epoch, high resolution spectroscopic observations (R=40000, corresponding to 7.5 km/s) of the optical afterglow of GRB080319B (z=0.937), taken with UVES at the VLT. Thanks to the rapid response mode (RRM), we observed the afterglow just 8m:30s after the GRB onset when the magnitude was R ~ 12. This allowed us to obtain the best signal-to-noise, high resolution spectrum of a GRB afterglow ever (S/N per resolution element ~ 50). Two further RRM and target of opportunity observations were obtained starting 1.0 and 2.4 hours after the event, respectively. Four MgII absorption systems lying along the line of sight to the afterglow have been detected in the redshift range 0.5 < z < 0.8, most of them showing a complex structure featuring several components. Absorptions due to FeII, MgI and MnII are also present; they appear in four, two and one intervening absorbers, respectively. One out of four systems show a MgII2796 rest frame equivalent width larger than 1A. This confirms the excess of strong MgII absorbers compared to quasars, with dn/dz = 0.9, ~ 4 times larger than the one observed along quasar lines of sight. In addition, the analysis of multi-epoch, high-resolution spectra allowed us to exclude a significant variability in the column density of the single components of each absorber. Combining this result with estimates of the size of the emitting region, we can reject the hypothesis that the difference between GRB and QSO MgII absorbers is due to a different size of the emitting regions.Comment: 10 pages, 15 ps figures, submitted to MNRA

Dynamical Properties of z~2 Star Forming Galaxies and a Universal Star Formation Relation

We present the first comparison of the dynamical properties of different samples of z~1.4-3.4 star forming galaxies from spatially resolved imaging spectroscopy from SINFONI/VLT integral field spectroscopy and IRAM CO millimeter interferometry. Our samples include 16 rest-frame UV-selected, 16 rest-frame optically-selected and 13 submillimeter galaxies (SMGs). We find that restframe UV- and optically bright (K<20) z~2 star forming galaxies are dynamically similar, and follow the same velocity-size relation as disk galaxies at z~0. In the theoretical framework of rotating disks forming from dissipative collapse in dark matter halos, the two samples require a spin parameter ranging from 0.06 to 0.2. In contrast bright SMGs have larger velocity widths and are much more compact. Hence, SMGs have lower angular momenta and higher matter densities than either of the UV- or optically selected populations. This indicates that dissipative major mergers may dominate the SMGs population, resulting in early spheroids, and that the majority of UV/optically bright galaxies have evolved less violently [...]. These early disks may later evolve into spheroids via disk instabilities or mergers. Because of their small sizes and large densities, SMGs lie at the high surface density end of a universal (out to z=2.5) "Schmidt-Kennicutt" relation between gas surface density and star formation rate surface density with a slope of ~1.7.Comment: 14 pages, 3 figures, accepted for publication in ApJ, minor typos correcte