| 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. |
- Wang, Fei, et al.
(författare)
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Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level
- 2022
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Pigs are valuable large animal models for biomedical and genetic research, but insights into the tissue- and cell-type-specific transcriptome and heterogeneity remain limited. By leveraging single-cell RNA sequencing, we generate a multiple-organ single-cell transcriptomic map containing over 200,000 pig cells from 20 tissues/organs. We comprehensively characterize the heterogeneity of cells in tissues and identify 234 cell clusters, representing 58 major cell types. In-depth integrative analysis of endothelial cells reveals a high degree of heterogeneity. We identify several functionally distinct endothelial cell phenotypes, including an endothelial to mesenchymal transition subtype in adipose tissues. Intercellular communication analysis predicts tissue- and cell type-specific crosstalk between endothelial cells and other cell types through the VEGF, PDGF, TGF-beta, and BMP pathways. Regulon analysis of single-cell transcriptome of microglia in pig and 12 other species further identifies MEF2C as an evolutionally conserved regulon in the microglia. Our work describes the landscape of single-cell transcriptomes within diverse pig organs and identifies the heterogeneity of endothelial cells and evolutionally conserved regulon in microglia.
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| 3. |
- Gao, Jiacheng, et al.
(författare)
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Irvsp : To obtain irreducible representations of electronic states in the VASP
- 2021
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Ingår i: Computer Physics Communications. - : ELSEVIER. - 0010-4655 .- 1879-2944. ; 261
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Tidskriftsartikel (refereegranskat)abstract
- We present an open-source program irvsp, to compute irreducible representations of electronic states for all 230 space groups with an interface to the Vienna ab-initio Simulation Package. This code is fed with plane-wave-based wavefunctions (e.g. WAVECAR) and space group operators (listed in OUTCAR), which are generated by the VASP package. This program computes the traces of matrix presentations and determines the corresponding irreducible representations for all energy bands and all the k-points in the three-dimensional Brillouin zone. It also works with spin-orbit coupling (SOC), i.e., for double groups. It is in particular useful to analyze energy bands, their connectivities, and band topology, after the establishment of the theory of topological quantum chemistry. Accordingly, the associated library -irrep_bcs.a - is developed, which can be easily linked to by other ab-initio packages. In addition, the program has been extended to orthogonal tight-binding (TB) Hamiltonians, e.g. electronic or phononic TB Hamiltonians. A sister program is presented as well. Program summary Program title: irvsp CPC Library link to program files: http://doi.org/10.1763/y9ds5nnm2f.1 Licensing provisions: GNU Lesser General Public License Programming language: Fortran 90/77 Nature of problem: Determining irreducible representations for all energy bands and all the k-points in 230 space groups. It is in particular useful to analyze energy bands, their connectivities, and band topology. Solution method: By computing the traces of matrix presentations of space group operators for the eigen-wavefunctions at a certain k-point in a given space group, one can determine irreducible representations for them.
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| 4. |
- Shao, Xue-Feng, et al.
(författare)
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Polyvinylpyrrolidone (PVP)-enabled significant suppression of supercooling of erythritol for medium-temperature thermal energy storage
- 2022
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Ingår i: Journal of Energy Storage. - : Elsevier BV. - 2352-152X .- 2352-1538. ; 46, s. 103915-
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Tidskriftsartikel (refereegranskat)abstract
- The supercooling effect is deemed to be a crucial issue for thermal energy storage using phase change materials (PCMs). The exploration of promising additives plays a decisive role in effective suppression efforts for suppressing the supercooling effect of a PCM. The present work proposed a potential additive, polyvinylpyrrolidone (PVP), to reduce the supercooling of erythritol, which is the most promising polyol PCM candidate for medium temperature range. PVP with various loadings was dispersed in erythritol to make composites for the proof-of-concept tests. It was shown that the degree of supercooling of erythritol can be reduced significantly from over 64 ? to about 21 ? in the presence of only 1.0 wt.% PVP. Along with the mitigated supercooling effect, the addition of PVP also leads to an increase of the retrievable latent heat during crystallization, from ~187 J/g to ~224 J/g at the same minute PVP loading of 1.0 wt.%, by increasing the crystallinity of erythritol. The PVP-loaded erythritol composites exhibit little sacrifice in latent heat of fusion, i.e., only ~15% loss when the PVP loading reaches 6.0 wt.%. In addition, multiple tests confirmed that PVP can be dissolved in erythritol, thus desirable compatibility was obtained and the composites would have long-term reliability. This proposed additive enables an efficient and cost-effective way for improving the crystallization behaviors of erythritol (and other polyol PCMs) towards real-world applications.
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