The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an ...atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design.
This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific.
In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.
Hormones in the hypothalamus-pituitary-adrenal (HPA) axis mediate many of the bodily responses to stressors, yet there is no clear relationship between the levels of these hormones and ...stress-associated mental illnesses such as posttraumatic stress disorder (PTSD). Therefore, other hormones are likely to be involved in this effect of stress. Here we used a rodent model of PTSD in which rats repeatedly exposed to a stressor display heightened fear learning following auditory Pavlovian fear conditioning. Our results show that stress-related increases in circulating ghrelin, a peptide hormone, are necessary and sufficient for stress-associated vulnerability to exacerbated fear learning and these actions of ghrelin occur in the amygdala. Importantly, these actions are also independent of the classic HPA stress axis. Repeated systemic administration of a ghrelin receptor agonist enhanced fear memory but did not increase either corticotropin-releasing factor (CRF) or corticosterone. Repeated intraamygdala infusion of a ghrelin receptor agonist produced a similar enhancement of fear memory. Ghrelin receptor antagonism during repeated stress abolished stress-related enhancement of fear memory without blunting stress-induced corticosterone release. We also examined links between ghrelin and growth hormone (GH), a major downstream effector of the ghrelin receptor. GH protein was upregulated in the amygdala following chronic stress, and its release from amygdala neurons was enhanced by ghrelin receptor stimulation. Virus-mediated overexpression of GH in the amygdala was also sufficient to increase fear. Finally, virus-mediated overexpression of a GH receptor antagonist was sufficient to block the fear-enhancing effects of repeated ghrelin receptor stimulation. Thus, ghrelin requires GH in the amygdala to exert fear-enhancing effects. These results suggest that ghrelin mediates a novel branch of the stress response and highlight a previously unrecognized role for ghrelin and growth hormone in maladaptive changes following prolonged stress.
We present new full-sky temperature and polarization maps in five frequency bands from 23 to 94 GHz, based on data from the first five years of the Wilkinson Microwave Anisotropy Probe (WMAP) sky ...survey. The new maps are consistent with previous maps and are more sensitive. The five-year maps incorporate several improvements in data processing made possible by the additional years of data and by a more complete analysis of the instrument calibration and in-flight beam response. We present several new tests for systematic errors in the polarization data and conclude that W-band polarization data is not yet suitable for cosmological studies, but we suggest directions for further study. We do find that Ka-band data is suitable for use; in conjunction with the additional years of data, the addition of Ka band to the previously used Q- and V-band channels significantly reduces the uncertainty in the optical depth parameter, tau . Further scientific results from the five-year data analysis are presented in six companion papers and are summarized in Section 7 of this paper. With the five-year WMAP data, we detect no convincing deviations from the minimal six-parameter Lambda CDM model: a flat universe dominated by a cosmological constant, with adiabatic and nearly scale-invariant Gaussian fluctuations. Using WMAP data combined with measurements of Type Ia supernovae and Baryon Acoustic Oscillations in the galaxy distribution, we find (68% CL uncertainties): Omega b h 2 = 0.02267+0.00058 -0.00059, Omega c h 2 = 0.1131 ± 0.0034, Omega Lambda = 0.726 ± 0.015, ns = 0.960 ± 0.013, tau = 0.084 ± 0.016, and at k = 0.002 Mpc-1. From these we derive sigma 8 = 0.812 ± 0.026, H 0 = 70.5 ± 1.3 km s-1 Mpc-1, Omega b = 0.0456 ± 0.0015, Omega c = 0.228 ± 0.013, Omega m h 2 = 0.1358+0.0037 -0.0036, z reion = 10.9 ± 1.4, and t 0 = 13.72 ± 0.12 Gyr. The new limit on the tensor-to-scalar ratio is r < 0.22(95%CL), while the evidence for a running spectral index is insignificant, dns /dln k = -0.028 ± 0.020 (68% CL). We obtain tight, simultaneous limits on the (constant) dark energy equation of state and the spatial curvature of the universe: -0.14 < 1 + w < 0.12(95%CL) and -0.0179 < Omega k < 0.0081(95%CL). The number of relativistic degrees of freedom, expressed in units of the effective number of neutrino species, is found to be N eff = 4.4 ± 1.5 (68% CL), consistent with the standard value of 3.04. Models with N eff = 0 are disfavored at >99.5% confidence. Finally, new limits on physically motivated primordial non-Gaussianity parameters are -9 < f local NL < 111 (95% CL) and -151 < f equil NL < 253 (95% CL) for the local and equilateral models, respectively.
This paper reports a study of the full carbon (C-CO2) budget of the Australian continent, focussing on 1990–2011 in the context of estimates over two centuries. The work is a contribution to the ...RECCAP (REgional Carbon Cycle Assessment and Processes) project, as one of numerous regional studies. In constructing the budget, we estimate the following component carbon fluxes: net primary production (NPP); net ecosystem production (NEP); fire; land use change (LUC); riverine export; dust export; harvest (wood, crop and livestock) and fossil fuel emissions (both territorial and non-territorial). Major biospheric fluxes were derived using BIOS2 (Haverd et al., 2012), a fine-spatial-resolution (0.05°) offline modelling environment in which predictions of CABLE (Wang et al., 2011), a sophisticated land surface model with carbon cycle, are constrained by multiple observation types. The mean NEP reveals that climate variability and rising CO2 contributed 12 24 (1σ error on mean) and 68 15 TgC yr−1, respectively. However these gains were partially offset by fire and LUC (along with other minor fluxes), which caused net losses of 26 4 TgC yr−1 and 18 7 TgC yr−1, respectively. The resultant net biome production (NBP) is 36 29 TgC yr−1, in which the largest contributions to uncertainty are NEP, fire and LUC. This NBP offset fossil fuel emissions (95 6 TgC yr−1) by 38 30%. The interannual variability (IAV) in the Australian carbon budget exceeds Australia's total carbon emissions by fossil fuel combustion and is dominated by IAV in NEP. Territorial fossil fuel emissions are significantly smaller than the rapidly growing fossil fuel exports: in 2009–2010, Australia exported 2.5 times more carbon in fossil fuels than it emitted by burning fossil fuels.
Black holes generate collimated, relativistic jets, which have been observed in gamma-ray bursts (GRBs), microquasars, and at the center of some galaxies active galactic nuclei (AGN). How jet physics ...scales from stellar black holes in GRBs to the supermassive ones in AGN is still unknown. Here, we show that jets produced by AGN and GRBs exhibit the same correlation between the kinetic power carried by accelerated particles and the gamma-ray luminosity, with AGN and GRBs lying at the low- and high-luminosity ends, respectively, of the correlation. This result implies that the efficiency of energy dissipation in jets produced in black hole systems is similar over 10 orders of magnitude in jet power, establishing a physical analogy between AGN and GRBs.
We present new full-sky temperature maps in five frequency bands from 23 to 94 GHz, based on data from the first 3 years of the WMAP sky survey. The new maps are consistent with the first-year maps ...and are more sensitive. The 3 year maps incorporate several improvements in data processing made possible by the additional years of data and by a more complete analysis of the polarization signal. These include several new consistency tests as well as refinements in the gain calibration and beam response models. We employ two forms of multifrequency analysis to separate astrophysical foreground signals from the CMB, each of which improves on our first-year analyses. First, we form an improved "Internal Linear Combination" (ILC) map, based solely on WMAP data, by adding a bias-correction step and by quantifying residual uncertainties in the resulting map. Second, we fit and subtract new spatial templates that trace Galactic emission; in particular, we now use low-frequency WMAP data to trace synchrotron emission instead of the 408 MHz sky survey. The WMAP point source catalog is updated to include 115 new sources whose detection is made possible by the improved sky map sensitivity. We derive the angular power spectrum of the temperature anisotropy using a hybrid approach that combines a maximum likelihood estimate at low l (large angular scales) with a quadratic cross-power estimate for l > 30. The resulting multifrequency spectra are analyzed for residual point source contamination. At 94 GHz the unmasked sources contribute 128 plus or minus 27 mu K super(2) to l(l + 1)C sub(l)/2 capital pi at l = 1000. After subtracting this contribution, our best estimate of the CMB power spectrum is derived by averaging cross-power spectra from 153 statistically independent channel pairs. The combined spectrum is cosmic variance limited to l = 400, and the signal-to-noise ratio per l-mode exceeds unity up to l = 850. For bins of width Delta l/l = 3%, the signal-to-noise ratio exceeds unity up to l = 1000. The first two acoustic peaks are seen at / = 220.8 plus or minus 0.7 and / = 530.9 plus or minus 3.8, respectively, while the first two troughs are seen at l = 412.4 plus or minus 1.9 and l = 675.2 plus or minus 11.1. The rise to the third peak is unambiguous; when the WMAP data are combined with higher resolution CMB measurements, the existence of a third acoustic peak is well established. Spergel et al. use the 3 year temperature and polarization data to constrain cosmological model parameters. A simple six-parameter ACDM model continues to fit CMB data and other measures of large-scale structure remarkably well. The new polarization data produce a better measurement of the optical depth to reionization, tau = 0.089 plus or minus 0.03. This new and tighter constraint on tau helps break a degeneracy with the scalar spectral index, which is now found to be n sub(S) = 0.960 plus or minus 0.016. If additional cosmological data sets are included in the analysis, the spectral index is found to be n sub(S) = 0.947 plus or minus 0.015.
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by ...single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
We present an investigation of the relationship between giant molecular cloud (GMC) properties and the associated stellar clusters in the nearby flocculent galaxy NGC 7793. We combine the star ...cluster catalogue from the HST LEGUS (Legacy ExtraGalactic UV Survey) programme with the 15 pc resolution ALMA CO(2-1) observations. We find a strong spatial correlation between young star clusters and GMCs such that all clusters still associated with a GMC are younger than 11 Myr and display a median age of 2 Myr. The age distribution increases gradually as the cluster-GMC distance increases, with star clusters that are spatially unassociated with molecular gas exhibiting a median age of 7 Myr. Thus, star clusters are able to emerge from their natal clouds long before the time-scale required for clouds to disperse. To investigate if the hierarchy observed in the stellar components is inherited from the GMCs, we quantify the amount of clustering in the spatial distributions of the components and find that the star clusters have a fractal dimension slope of -0.35 +/- 0.03, significantly more clustered than the molecular cloud hierarchy with slope of -0.18 +/- 0.04 over the range 40-800 pc. We find, however, that the spatial clustering becomes comparable in strength for GMCs and star clusters with slopes of -0.44 +/- 0.03 and -0.45 +/- 0.06, respectively, when we compare massive (> 10(5) M-circle dot) GMCs to massive and young star clusters. This shows that massive star clusters trace the same hierarchy as their parent GMCs, under the assumption that the star formation efficiency is a few per cent.
We present new kinematic measurements and modeling of a sample of 116 young stars in the central parsec of the Galaxy in order to investigate the properties of the young stellar disk. The ...measurements were derived from a combination of speckle and laser guide star adaptive optics imaging and integral field spectroscopy from the Keck telescopes. Compared to earlier disk studies, the most important kinematic measurement improvement is in the precision of the accelerations in the plane of the sky, which have a factor of six smaller uncertainties (sigma ~ 10 mu as yr super(-2)). We have also added the first radial velocity measurements for eight young stars, increasing the sample at the largest radii (6"-2") by 25%. We derive the ensemble properties of the observed stars using Monte Carlo simulations of mock data. There is one highly significant kinematic feature (~20sigma), corresponding to the well-known clockwise disk, and no significant feature is detected at the location of the previously claimed counterclockwise disk. The true disk fraction is estimated to be ~20%, a factor of ~2.5 lower than previous claims, suggesting that we may be observing the remnant of what used to be a more densely populated stellar disk. The similarity in the kinematic properties of the B stars and the O/WR stars suggests a common star formation event. The intrinsic eccentricity distribution of the disk stars is unimodal, with an average value of left angle bracketeright angle bracket = 0.27 + or - 0.07, which we show can be achieved through dynamical relaxation in an initially circular disk with a moderately top-heavy mass function.
Abstract Background Anxiety frequently accompanies low-grade inflammation-associated conditions like depression, insulin resistance, coronary heart disease and metabolic syndrome. The association ...between anxiety and low-grade inflammation is, unlike between depression and low-grade inflammation, a very sparsely studied area in general populations. The aim of the present study was to investigate whether anxiety symptoms as well as comorbid anxiety and depressive symptoms are associated with low-grade inflammation at population level. Methods The general population-based Northern Finland 1966 Birth Cohort was followed until age 31 ( n = 2688 males and 2837 females), when the highly sensitive CRP concentrations were measured. Anxiety and depressive symptoms were defined by Hopkins Symptom Checklist-25 (HSCL-25). Results After adjusting for confounders, logistic regression analyses showed that anxiety symptoms alone increased the probability for elevated hs-CRP levels (> 3.0 mg/L) in males over two-fold (2.19 CI 95% 1.08–4.46), while comorbid anxiety and depressive symptoms caused a 1.7-fold (1.76 CI 95% 1.13–2.74) increase in the probability for elevated hs-CRP levels (1.0–3.0 mg/L). Conclusions Our results support the hypothesis that anxiety as well as comorbid anxiety and depression can be associated with an increased risk for low-grade inflammation in males at population level.
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