Comprehensive evaluation of deconvolution methods for human brain gene expression

Transcriptome deconvolution aims to estimate the cellular composition of an RNA sample from its gene expression data, which in turn can be used to correct for composition differences across samples. The human brain is unique in its transcriptomic diversity, and comprises a complex mixture of cell-types, including transcriptionally similar subtypes of neurons. Here, we carry out a comprehensive evaluation of deconvolution methods for human brain transcriptome data, and assess the tissue-specificity of our key observations by comparison with human pancreas and heart. We evaluate eight transcriptome deconvolution approaches and nine cell-type signatures, testing the accuracy of deconvolution using in silico mixtures of single-cell RNA-seq data, RNA mixtures, as well as nearly 2000 human brain samples. Our results identify the main factors that drive deconvolution accuracy for brain data, and highlight the importance of biological factors influencing cell-type signatures, such as brain region and in vitro cell culturing.Gavin J. Sutton, Daniel Poppe, Rebecca K. Simmons, Kieran Walsh, Urwah Nawaz, Ryan Lister, Johann A. Gagnon-Bartsch, Irina Voineag

Branching Fractions for D0 -> K+K- and D0 -> pi+pi-, and a Search for CP Violation in D0 Decays

Using the large hadroproduced charm sample collected in experiment E791 at Fermilab, we have measured ratios of branching fractions for the two-body singly-Cabibbo-suppressed charged decays of the D0: (D0 -> KK)/(D0 -> Kpi) = 0.109 +- 0.003 +- 0.003, (D0 -> pipi)/(D0 -> Kpi) = 0.040 +- 0.002 +- 0.003, and (D0 -> KK)/(D0 -> pipi) = 2.75 +- 0.15 +- 0.16. We have looked for differences in the decay rates of D0 and D0bar to the CP eigenstates K+K- and pi+pi-, and have measured the CP asymmetry parameters A_CP(K+K-) = -0.010 +- 0.049 +- 0.012 and A_CP(pi+pi-) = -0.049 +- 0.078 +- 0.030, both consistent with zero.Comment: 10 Postscript pages, including 2 figures. Submitted to Phys. Lett.

Coastal restoration success via emergent trait-mimicry is context dependent

Coastal ecosystems provide vital ecosystem functions and services, but have been rapidly degrading due to human impacts. Restoration is increasingly considered key to reversing these losses, but is often unsuccessful. Recent work on seagrasses and salt marsh cordgrasses highlights that restoration yields can be greatly enhanced by temporarily mimicking key emergent traits. These traits are not expressed by individual seedlings or small clones, but emerge in clumped individuals or large clones to locally suppress environmental stress, causing establishment thresholds where such density-dependent self-facilitation is important for persistence. It remains unclear, however, to what extent the efficacy of restoration via emergent trait-based mimicry depends on the intensity of stressors. We test this in a restoration experiment with the temperate seagrass Zostera marina at four sites (Finland, Sweden, UK, USA) with contrasting hydrodynamic regimes, where we simulated dense roots mats or vegetation canopies with biodegradable structural mimics. Results show that by mimicking sediment-stabilizing root mats, seagrass transplant survival, growth and expansion was strongly enhanced in hydrodynamically exposed environments. However, these positive effects decreased and turned negative under benign conditions, while mimics insufficiently mitigated physical stress in extremely exposed environments, illustrating upper and lower limits of the application. Furthermore, we found that aboveground structures, designed to mimic stiff rather than flexible vegetation canopies, underperformed compared to belowground mimics. Our findings emphasize the importance of understanding the conditions at the restoration site, species-specific growth requirements, and self-facilitating traits that organisms may express when applying emergent trait-mimicry as a tool to improve restoration success

Asymmetries between the production of D+ and D- mesons from 500 GeV/c pi- nucleon interactions as a function of xF and pt**2

We present asymmetries between the production of D+ and D- mesons in Fermilab experiment E791 as a function of xF and pt**2. The data used here consist of 74,000 fully-reconstructed charmed mesons produced by a 500 GeV/c pi- beam on C and Pt foils. The measurements are compared to results of models which predict differences between the production of heavy-quark mesons that have a light quark in common with the beam (leading particles) and those that do not (non-leading particles). While the default models do not agree with our data, we can reach agreement with one of them, PYTHIA, by making a limited number of changes to parameters used

Search for Rare and Forbidden Dilepton Decays of the D+, Ds, and D0 Charmed Mesons

We report the results of a search for flavor-changing neutral current, lepton-flavor violating, and lepton-number violating decays of D+, Ds, and D0 mesons (and their antiparticles) into modes containing muons and electrons. Using data from Fermilab charm hadroproduction experiment E791, we examine the pi,l,l and K,l,l decay modes of D+ and Ds and the l+l- decay modes of D0. No evidence for any of these decays is found. Therefore, we present branching-fraction upper limits at 90% confidence level for the 24 decay modes examined. Eight of these modes have no previously reported limits, and fourteen are reported with significant improvements over previously published results.Comment: 12 pages, 3 figures, LaTeX, elsart.cls, epsf.sty, amsmath.sty Submitted to Physics Letters

Search for CP Violation in Charged D Meson Decays

We report results of a search for CP violation in the singly Cabibbo-suppressed decays D+ -> K- K+ pi+, phi pi+, K*(892)0 K+, and pi- pi+ pi+ based on data from the charm hadroproduction experiment E791 at Fermilab. We search for a difference in the D+ and D- decay rates for each of the final states. No evidence for a difference is seen. The decay rate asymmetry parameters A(CP), defined as the difference in the D+ and D- decay rates divided by the sum of the decay rates, are measured to be: A(CP)(K K pi) = -0.014 +/- 0.029, A(CP)(phi pi) = -0.028 +/- 0.036, A(CP)(K*(892) K) = -0.010 +/- 0.050, and A(CP)(pi pi pi) = -0.017 +/- 0.042.Comment: 13 pages, 5 figures, 1 table; Elsevier LaTe

Measurement of the form-factor ratios for D+ --> K* l nu

The form factor ratios rv=V(0)/A1(0), r2=A2(0)/A1(0) and r3=A3(0)/A1(0) in the decay D+ --> K* l nu, K* -->K-pi+ have been measured using data from charm hadroproduction experiment E791 at Fermilab. From 3034 (595) signal (background) events in the muon channel, we obtain rv=1.84+-0.11+-0.09, r2=0.75+-0.08+-0.09 and, as a first measurement of r3, we find 0.04+-0.33 +-0.29. The values of the form factor ratios rv and r2 measured for the muon channel are combined with the values of rv and r2 that we have measured in the electron channel. The combined E791 results for the muon and electron channels are rv=1.87+-0.08+-0.07 and r2=0.73+-0.06+-0.08.Comment: 9 pages + 3 figures ; submitted to PL

Differential cross sections, charge production asymmetry, and spin-density matrix elements for D*(2010) produced in 500 GeV/c pi^- nucleon interactions

We report differential cross sections for the production of D*(2010) produced in 500 GeV/c pi^- nucleon interactions from experiment E791 at Fermilab, as functions of Feynman-x (x_F) and transverse momentum squared (p_T^2). We also report the D* +/- charge asymmetry and spin-density matrix elements as functions of these variables. Investigation of the spin-density matrix elements shows no evidence of polarization. The average values of the spin alignment are \eta= 0.01 +- 0.02 and -0.01 +- 0.02 for leading and non-leading particles, respectively.Comment: LaTeX2e (elsart.cls). 13 pages, 6 figures (eps files). Submitted to Physics Letters

Mass Splitting and Production of Σc0\Sigma_c^0 and Σc++\Sigma_c^{++} Measured in 500GeV500 {GeV} π−−\pi^- -N Interactions

From a sample of $2722 \pm 78$ $\Lambda_c^+$ decaying to the $pK^-\pi^+$ final state, we have observed, in the hadroproduction experiment E791 at Fermilab, $143 \pm 20$ $\Sigma_c^0$ and $122 \pm 18$ $\Sigma_c^{++}$ through their decays to $\Lambda_c^+ \pi^{\pm}$. The mass difference $M(\Sigma_c^0) - M(\Lambda_c^+$) is measured to be $(167.38\pm 0.29\pm 0.15) {MeV}$; for $M(\Sigma_c^{++}) - M(\Lambda_c^+)$, we find $(167.76\pm 0.29\pm0.15) {MeV}$. The rate of $\Lambda_c^+$ production from decays of the $\Sigma_c$ triplet is (22\pm 2\pm 3) {%} of the total $\Lambda_c^+$ production assuming equal rate of production from all three, as measured for $\Sigma_c^0$ and $\Sigma_c^{++}$. We do not observe a statistically significant $\Sigma_c$ baryon-antibaryon production asymmetry. The $x_F$ and $p_t^2$ spectra of $\Lambda_c^+$ from $\Sigma_c$ decays are observed to be similar to those for all $\Lambda_c^+$'s produced.Comment: 15 pages, uuencoded postscript 3 figures uuencoded, tar-compressed fil

Mimicry of emergent traits amplifies coastal restoration success

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