| 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. |
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| 3. |
- Duong, Thien C., et al.
(författare)
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Revisiting thermodynamics and kinetic diffusivities of uranium-niobium with Bayesian uncertainty analysis
- 2016
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Ingår i: CALPHAD-COMPUTER COUPLING OF PHASE DIAGRAMS AND THERMOCHEMISTRY. - : Elsevier. - 0364-5916. ; 55, s. 219-230
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Tidskriftsartikel (refereegranskat)abstract
- In this work, thermodynamic and kinetic diffusivities of uranium-niobium (U-Nb) are re-assessed by means of the CALPHAD (CALculation of PHAse Diagram) methodology. In order to improve the consistency and reliability of the assessments, first-principles calculations are coupled with CALPHAD. In particular, heats of formation of gamma-U-Nb are estimated and verified using various density-functional theory (DFT) approaches. These thermochemistry data are then used as constraints to guide the thermodynamic optimization process in such a way that the mutual-consistency between first-principles calculations and CALPHAD assessment is satisfactory. In addition, long-term aging experiments are conducted in order to generate new phase equilibria data at the gamma(2)/alpha + gamma(2) boundary. These data are meant to verify the thermodynamic model. Assessment results are generally in good agreement with experiments and previous calculations, without showing the artifacts that were observed in previous modeling. The mutual-consistent thermodynamic description is then used to evaluate atomic mobility and diffusivity of gamma-U-Nb. Finally, Bayesian analysis is conducted to evaluate the uncertainty of the thermodynamic model and its impact on the system's phase stability.
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| 4. |
- Muus, Christoph, et al.
(författare)
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
- 2021
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Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 27:3, s. 546-559
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Tidskriftsartikel (refereegranskat)abstract
- Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2(+)TMPRSS2(+) cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention. An integrated analysis of over 100 single-cell and single-nucleus transcriptomics studies illustrates severe acute respiratory syndrome coronavirus 2 viral entry gene coexpression patterns across different human tissues, and shows association of age, smoking status and sex with viral entry gene expression in respiratory cell populations.
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| 5. |
- Rauh, Sebastian Felix, 1986-
(författare)
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Exploring the Potential of Head Worn Displays for Manual Work Tasks in Industrial Environments
- 2017
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis I explore the potential of modern Head-Worn Displays for aiding manual work tasks in the manufacturing industries. In such settings, workers are already supported by using mobile hand-held devices that show instructions and enable the worker to document work tasks. However, the most important disadvantage of hand-held devices is that users need to put them aside when performing tasks that require both of their hands. The current generation of Head-Worn Displays promises hands-free usage with little added complexity and also enables the augmentation of workers’ vision,thereby supporting the work task in a more effective and efficient way.For assessing the potential of Head-Worn Displays on factory floors, a series of studies has been conducted. The studies have been carried out directly on the production line of a German car manufacturer together with workers or in-lab, depending on the study goals. Together with workers and managers in the industrial settings we identified two work tasks whereby support for Head-Worn Displays showed good potential for increasing productivity, quality and worker comfort. The Head-Worn Display support was improved in an iterative manner within a Human-Centred Design approach.The thesis contributes with experiences on introducing Head-Worn Displays in real world settings and for long time periods. The recorded productivity increases attributed to the Head-Worn Displays are discussed, along with worker and manager feedback. For long-term use on a factory floor, extending battery operating time was found to be of central importance. CPU and Camera were identified as the most energy consuming devices and an approach to address that is presented. A benchmark suite is introduced to enable designers, developers, and project managers to make informed decisions when selecting Head-Worn Displays. Finally, a theoretical discussion of Head-Worn Displays is presented by situating them in a sense-based Augmented Reality taxonomy, I proposed.
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| 6. |
- Szykowska, Aleksandra, et al.
(författare)
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Selection and structural characterization of anti-TREM2 scFvs that reduce levels of shed ectodomain
- 2021
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 29:11, s. 1241-
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Tidskriftsartikel (refereegranskat)abstract
- Mutations in TREM2, a receptor expressed by microglia in the brain, are associated with an increased risk of neurodegeneration, including Alzheimer's disease. Numerous studies support a role for TREM2 in sensing damaging stimuli and triggering signaling cascades necessary for neuroprotection. Despite its significant role, ligands and regulators of TREM2 activation, and the mechanisms governing TREM2-dependent responses and its cleavage from the membrane, remain poorly characterized. Here, we present phage display generated antibody single-chain variable fragments (scFvs) to human TREM2 immunoglobulin-like domain. Co-crystal structures revealed the binding of two scFvs to an epitope on the TREM2 domain distal to the putative ligand-binding site. Enhanced functional activity was observed for oligomeric scFv species, which inhibited the production of soluble TREM2 in a HEK293 cell model. We hope that detailed characterization of their epitopes and properties will facilitate the use of these renewable binders as structural and functional biology tools for TREM2 research.
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