| 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. |
- Borga, Magnus, et al.
(författare)
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Reproducibility and repeatability of MRI-based body composition analysis
- 2020
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Ingår i: Magnetic Resonance in Medicine. - : WILEY. - 0740-3194 .- 1522-2594. ; 84:6, s. 3146-3156
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Tidskriftsartikel (refereegranskat)abstract
- Purpose There is an absence of reproducibility studies on MRI-based body composition analysis in current literature. Therefore, the aim of this study was to investigate the between-scanner reproducibility and the repeatability of a method for MRI-based body composition analysis. Methods Eighteen healthy volunteers of varying body mass index and adiposity were each scanned twice on five different 1.5T and 3T scanners from three different vendors. Two-point Dixon neck-to knee images and two additional liver scans were acquired with similar protocols. Visceral adipose tissue (VAT) volume, abdominal subcutaneous adipose tissue (ASAT) volume, thigh muscle volume, and muscle fat infiltration (MFI) in the thigh muscle were measured. Liver proton density fat fraction (PDFF) was assessed using two different methods, the scanner vendors 6-point method and an in-house 2-point method. Within-scanner test-retest repeatability and between-scanner reproducibility were calculated using analysis of variance. Results Repeatability coefficients were 13 centiliters (cl) (VAT), 24 cl (ASAT), 17 cl (total thigh muscle volume), 0.53% (MFI), and 1.27-1.37% for liver PDFF. Reproducibility coefficients were 24 cl (VAT), 42 cl (ASAT), 31 cl (total thigh muscle volume), 1.44% (MFI), and 2.37-2.40% for liver PDFF. Conclusion For all measures except MFI, the within-scanner repeatability explained much of the overall reproducibility. The two methods for measuring liver fat had similar reproducibility. This study showed that the investigated method eliminates effects due to scanner differences. The results can be used for power calculations in clinical studies or to better understand the scanner-induced variability in clinical applications.
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| 3. |
- Dussex, Nicolas, et al.
(författare)
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Moose genomes reveal past glacial demography and the origin of modern lineages
- 2020
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impacts of these climate fluctuations on ungulates from high latitudes have been little explored. Here, we assemble a de-novo genome for the European moose (Alces alces) and analyse it together with re-sequenced nuclear genomes and ancient and modern mitogenomes from across the moose range in Eurasia and North America.Results: We found that moose demographic history was greatly influenced by glacial cycles, with demographic responses to the Pleistocene/Holocene transition similar to other temperate ungulates. Our results further support that modern moose lineages trace their origin back to populations that inhabited distinct glacial refugia during the Last Glacial Maximum (LGM). Finally, we found that present day moose in Europe and North America show low to moderate inbreeding levels resulting from post-glacial bottlenecks and founder effects, but no evidence for recent inbreeding resulting from human-induced population declines.Conclusions: Taken together, our results highlight the dynamic recent evolutionary history of the moose and provide an important resource for further genomic studies.
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| 4. |
- Virhammar, Johan, et al.
(författare)
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Cerebral Perfusion Does Not Increase after Shunt Surgery for Normal Pressure Hydrocephalus
- 2020
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Ingår i: Journal of Neuroimaging. - : Wiley. - 1051-2284 .- 1552-6569. ; 30:3, s. 303-307
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND AND PURPOSE: Cerebral blood flow (CBF) has been reported to increase after shunt surgery in patients with idiopathic normal pressure hydrocephalus (iNPH). The aims of this study were to investigate if CBF, measured using the noninvasive perfusion MRI method arterial spin labeling (ASL), increased after shunt surgery, if postoperative change in CBF correlated with improvement in symptoms, and if baseline CBF data correlated with postoperative outcome.METHODS: Twenty-three patients with iNPH were prospectively included and examined with MRI of the brain and clinical tests of symptoms at baseline. Eighteen of the patients were treated with shunt implantation and were reexamined with clinical tests and MRI 3 months postoperatively. The MRI protocol included a pseudo-continuous ASL sequence for perfusion imaging. The perfusion was measured in 12 manually drawn regions of interest (ROIs).RESULTS: In the whole sample, CBF did not increase after shunting in any ROI. Preoperative CBF in medial frontal cortex correlated with an improvement in urinary incontinence after shunt surgery, r = .53, P = .022. There were no correlations between change in CBF and change in clinical symptoms postoperatively.CONCLUSIONS: The clinical value of ASL in the work-up of patients with iNPH is uncertain. In this study, ASL could not predict outcome after shunt surgery and there were no correlations between change in CBF and change in clinical symptoms after shunt surgery.
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