| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Spertus, John A, et al.
(författare)
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Health-Status Outcomes with Invasive or Conservative Care in Coronary Disease.
- 2020
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Ingår i: New England Journal of Medicine. - 0028-4793 .- 1533-4406. ; 382:15, s. 1408-1419
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: In the ISCHEMIA trial, an invasive strategy with angiographic assessment and revascularization did not reduce clinical events among patients with stable ischemic heart disease and moderate or severe ischemia. A secondary objective of the trial was to assess angina-related health status among these patients.METHODS: We assessed angina-related symptoms, function, and quality of life with the Seattle Angina Questionnaire (SAQ) at randomization, at months 1.5, 3, and 6, and every 6 months thereafter in participants who had been randomly assigned to an invasive treatment strategy (2295 participants) or a conservative strategy (2322). Mixed-effects cumulative probability models within a Bayesian framework were used to estimate differences between the treatment groups. The primary outcome of this health-status analysis was the SAQ summary score (scores range from 0 to 100, with higher scores indicating better health status). All analyses were performed in the overall population and according to baseline angina frequency.RESULTS: At baseline, 35% of patients reported having no angina in the previous month. SAQ summary scores increased in both treatment groups, with increases at 3, 12, and 36 months that were 4.1 points (95% credible interval, 3.2 to 5.0), 4.2 points (95% credible interval, 3.3 to 5.1), and 2.9 points (95% credible interval, 2.2 to 3.7) higher with the invasive strategy than with the conservative strategy. Differences were larger among participants who had more frequent angina at baseline (8.5 vs. 0.1 points at 3 months and 5.3 vs. 1.2 points at 36 months among participants with daily or weekly angina as compared with no angina).CONCLUSIONS: In the overall trial population with moderate or severe ischemia, which included 35% of participants without angina at baseline, patients randomly assigned to the invasive strategy had greater improvement in angina-related health status than those assigned to the conservative strategy. The modest mean differences favoring the invasive strategy in the overall group reflected minimal differences among asymptomatic patients and larger differences among patients who had had angina at baseline. (Funded by the National Heart, Lung, and Blood Institute and others; ISCHEMIA ClinicalTrials.gov number, NCT01471522.).
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| 3. |
- Anton, Rikard, et al.
(författare)
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A fully discrete approximation of the one-dimensional stochastic heat equation
- 2020
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Ingår i: IMA Journal of Numerical Analysis. - : Oxford University Press. - 0272-4979 .- 1464-3642. ; 40:1, s. 247-284
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Tidskriftsartikel (refereegranskat)abstract
- A fully discrete approximation of the one-dimensional stochastic heat equation driven by multiplicative space–time white noise is presented. The standard finite difference approximation is used in space and a stochastic exponential method is used for the temporal approximation. Observe that the proposed exponential scheme does not suffer from any kind of CFL-type step size restriction. When the drift term and the diffusion coefficient are assumed to be globally Lipschitz this explicit time integrator allows for error bounds in Lq(Ω), for all q ≥ 2, improving some existing results in the literature. On top of this we also prove almost sure convergence of the numerical scheme. In the case of nonglobally Lipschitz coefficients, under a strong assumption about pathwise uniqueness of the exact solution, convergence in probability of the numerical solution to the exact solution is proved. Numerical experiments are presented to illustrate the theoretical results.
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| 4. |
- Baer, Donald R., et al.
(författare)
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XPS guide: Charge neutralization and binding energy referencing for insulating samples
- 2020
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Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : A V S AMER INST PHYSICS. - 0734-2101 .- 1520-8559. ; 38:3
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Tidskriftsartikel (refereegranskat)abstract
- This guide deals with methods to control surface charging during XPS analysis of insulating samples and approaches to extracting useful binding energy information. The guide summarizes the causes of surface charging, how to recognize when it occurs, approaches to minimize charge buildup, and methods used to adjust or correct XPS photoelectron binding energies when charge control systems are used. There are multiple ways to control surface charge buildup during XPS measurements, and examples of systems on advanced XPS instruments are described. There is no single, simple, and foolproof way to extract binding energies on insulating material, but advantages and limitations of several approaches are described. Because of the variety of approaches and limitations of each, it is critical for researchers to accurately describe the procedures that have been applied in research reports and publications.
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| 5. |
- Ben-David, Yael, et al.
(författare)
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RIC3, the cholinergic anti-inflammatory pathway, and neuroinflammation
- 2020
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Ingår i: International Immunopharmacology. - : ELSEVIER. - 1567-5769 .- 1878-1705. ; 83
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Tidskriftsartikel (refereegranskat)abstract
- Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels having many functions including inflammation control, as part of the cholinergic anti-inflammatory pathway. Genome wide association studies implicated RIC3, a chaperone of nAChRs, in multiple sclerosis (MS), a neuroinflammatory disease. To understand the involvement of RIC3 in inflammatory diseases we examined its expression, regulation, and function in activated immune cells. Our results show that immune activation leads to dynamic changes in RIC3 expression, in a mouse model of MS and in human lymphocytes and macrophages. We also show similarities in the expression dynamics of RIC3 and CHRNA7, encoding for the alpha 7 nAChR subunit. Homomeric alpha 7 nAChRs were shown to mediate the anti-inflammatory effects of cholinergic agonists. Thus, similarity in expression dynamics between RIC3 and CHRNA7 is suggestive of functional concordance. Indeed, siRNA mediated silencing of RIC3 in a mouse macrophage cell line eliminates the anti-inflammatory effects of cholinergic agonists. Furthermore, we show increased average expression of RIC3 and CHRNA7 in lymphocytes from MS patients, and a strong correlation between expression levels of these two genes in MS patients but not in healthy donors. Together, our results are consistent with a role for RIC3 and for the mechanisms regulating its expression in inflammatory processes and in neuroinflammatory diseases.
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| 6. |
- Chen, C. C., et al.
(författare)
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Drift-preserving numerical integrators for stochastic Hamiltonian systems
- 2020
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Ingår i: Advances in Computational Mathematics. - : Springer Science and Business Media LLC. - 1019-7168 .- 1572-9044. ; 46:2
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Tidskriftsartikel (refereegranskat)abstract
- The paper deals with numerical discretizations of separable nonlinear Hamiltonian systems with additive noise. For such problems, the expected value of the total energy, along the exact solution, drifts linearly with time. We present and analyze a time integrator having the same property for all times. Furthermore, strong and weak convergence of the numerical scheme along with efficient multilevel Monte Carlo estimators are studied. Finally, extensive numerical experiments illustrate the performance of the proposed numerical scheme.
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| 7. |
- Cohen, David, 1977, et al.
(författare)
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Exponential integrators for stochastic Maxwell's equations driven by Itô noise
- 2020
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 1090-2716 .- 0021-9991. ; 410
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Tidskriftsartikel (refereegranskat)abstract
- This article presents explicit exponential integrators for stochastic Maxwell's equations driven by both multiplicative and additive noises. By utilizing the regularity estimate of the mild solution, we first prove that the strong order of the numerical approximation is [Formula presented] for general multiplicative noise. Combining a proper decomposition with the stochastic Fubini's theorem, the strong order of the proposed scheme is shown to be 1 for additive noise. Moreover, for linear stochastic Maxwell's equation with additive noise, the proposed time integrator is shown to preserve exactly the symplectic structure, the evolution of the energy as well as the evolution of the divergence in the sense of expectation. Several numerical experiments are presented in order to verify our theoretical findings.
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| 8. |
- Cohen, David, et al.
(författare)
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High order numerical integrators for single integrand Stratonovich SDEs
- 2020
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Ingår i: Applied Numerical Mathematics. - : Elsevier BV. - 0168-9274 .- 1873-5460. ; 158, s. 264-270
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Tidskriftsartikel (refereegranskat)abstract
- We show that applying any deterministic B-series method of order pd with a random step size to single integrand SDEs gives a numerical method converging in the mean-square and weak sense with order left perpendicular pd/2 right perpendicular. As an application, we derive high order energy-preserving methods for stochastic Poisson systems as well as further geometric numerical schemes for this wide class of Stratonovich SDEs. (C) 2020 The Author(s). Published by Elsevier B.V. on behalf of IMACS.
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| 9. |
- Hasselquist, Sten, et al.
(författare)
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Exploring the stellar age distribution of the milky way bulge using APOGEE
- 2020
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Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 901:2
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Tidskriftsartikel (refereegranskat)abstract
- We present stellar age distributions of the Milky Way bulge region using ages for ∼6000 high-luminosity (log(g)< 2.0), metal-rich ([Fe/H] ≥ -0.5) bulge stars observed by the Apache Point Observatory Galactic Evolution Experiment. Ages are derived using The Cannon label-transfer method, trained on a sample of nearby luminous giants with precise parallaxes for which we obtain ages using a Bayesian isochrone-matching technique. We find that the metal-rich bulge is predominantly composed of old stars (>8 Gyr). We find evidence that the planar region of the bulge (ZGC| 0.25 kpc) is enriched in metallicity, Z, at a faster rate (dZ/dt ∼ 0.0034 Gyr-1) than regions farther from the plane (dZ/dt ∼ 0.0013 Gyr-1 at | ZGC| > 1.00 kpc). We identify a nonnegligible fraction of younger stars (age ∼2-5 Gyr) at metallicities of +0.2 < [Fe/H] < +0.4. These stars are preferentially found in the plane (ZGC| ≤ 0.25 kpc) and at R cy ≈ 2-3 kpc, with kinematics that are more consistent with rotation than are the kinematics of older stars at the same metallicities. We do not measure a significant age difference between stars found inside and outside the bar. These findings show that the bulge experienced an initial starburst that was more intense close to the plane than far from the plane. Then, star formation continued at supersolar metallicities in a thin disk at 2 kpc ≲ R cy ≲ 3 kpc until ∼2 Gyr ago.
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| 10. |
- Moiseev, Sergey, et al.
(författare)
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2020 international consensus on ANCA testing beyond systemic vasculitis
- 2020
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Ingår i: Autoimmunity Reviews. - : Elsevier BV. - 1568-9972. ; 19:9
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Forskningsöversikt (refereegranskat)abstract
- This document follows up on a 2017 revised international consensus on anti-neutrophil cytoplasm antibodies (ANCA) testing in granulomatosis with polyangiitis and microscopic polyangiitis and focuses on the clinical and diagnostic value of ANCA detection in patients with connective tissue diseases, idiopathic interstitial pneumonia, autoimmune liver diseases, inflammatory bowel diseases, anti-glomerular basement membrane (GBM) disease, infections, malignancy, and during drug treatment. Current evidence suggests that in certain settings beyond systemic vasculitis, ANCA may have clinical, pathogenic and/or diagnostic relevance. Antigen-specific ANCA targeting proteinase-3 and myeloperoxidase should be tested by solid phase immunoassays in any patient with clinical features suggesting ANCA-associated vasculitis and in all patients with anti-GBM disease, idiopathic interstitial pneumonia, and infective endocarditis associated with nephritis, whereas in patients with other aforementioned disorders routine ANCA testing is not recommended. Among patients with autoimmune liver diseases or inflammatory bowel diseases, ANCA testing may be justified in patients with suspected autoimmune hepatitis type 1 who do not have conventional autoantibodies or in case of diagnostic uncertainty to discriminate ulcerative colitis from Crohn's disease. In these cases, ANCA should be tested by indirect immunofluorescence as the target antigens are not yet well characterized. Many questions concerning the optimal use of ANCA testing in patients without ANCA-associated vasculitis remain to be answered.
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