| 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. |
- 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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| 3. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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