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- 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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| 7. |
- Leitner, Torsten, 1979-, et al.
(författare)
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The CoESCA station at BESSY: Auger electron–photoelectron coincidences from surfaces demonstrated for Ag MNN
- 2021
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 250
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we present the CoESCA station for electron–electron coincidence spectroscopy from surfaces, built in a close collaboration between Uppsala University and Helmholtz-Zentrum Berlin at the BESSY II synchrotron facility in Berlin, Germany. We start with a detailed overview of previous work in the field of electron–electron coincidences, before we describe the CoESCA setup and its design parameters. The system is capable of recording shot-to-shot resolved 6D coincidence datasets, i.e. the kinetic energy and the two take off angles for both coincident electrons. The mathematics behind extracting and analysing these multi-dimensional coincidence datasets is introduced, with a focus on coincidence statistics, resulting in fundamental limits of the signal-to-noise ratio and its implications for acquisition times and the size of the raw data stream. The functionality of the CoESCA station is demonstrated for the example of Auger electron–photoelectron coincidences from silver surfaces for photoelectrons from the Ag 3d core levels and their corresponding MNN Auger electrons. The Auger spectra originating from the different core levels, 3d and 3d could be separated and further, the two-hole state energy distributions were determined for these Auger decay channels.
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| 8. |
- Li, Jian-Yang, et al.
(författare)
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Ejecta from the DART-produced active asteroid Dimorphos
- 2023
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 616, s. 452-456
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Tidskriftsartikel (refereegranskat)abstract
- Some active asteroids have been proposed to be formed as a result of impact events1. Because active asteroids are generally discovered by chance only after their tails have fully formed, the process of how impact ejecta evolve into a tail has, to our knowledge, not been directly observed. The Double Asteroid Redirection Test (DART) mission of NASA2, in addition to having successfully changed the orbital period of Dimorphos3, demonstrated the activation process of an asteroid resulting from an impact under precisely known conditions. Here we report the observations of the DART impact ejecta with the Hubble Space Telescope from impact time T + 15 min to T + 18.5 days at spatial resolutions of around 2.1 km per pixel. Our observations reveal the complex evolution of the ejecta, which are first dominated by the gravitational interaction between the Didymos binary system and the ejected dust and subsequently by solar radiation pressure. The lowest-speed ejecta dispersed through a sustained tail that had a consistent morphology with previously observed asteroid tails thought to be produced by an impact4,5. The evolution of the ejecta after the controlled impact experiment of DART thus provides a framework for understanding the fundamental mechanisms that act on asteroids disrupted by a natural impact1,6.
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| 9. |
- Mikheeva, Olga, et al.
(författare)
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Aligned Multi-Task Gaussian Process
- 2022
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Ingår i: Proceedings of the 25th International Conference on Artificial Intelligence and Statistics, AISTATS 2022. - : ML Research Press. ; , s. 2970-2988
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Konferensbidrag (refereegranskat)abstract
- Multi-task learning requires accurate identification of the correlations between tasks. In real-world time-series, tasks are rarely perfectly temporally aligned; traditional multitask models do not account for this and subsequent errors in correlation estimation will result in poor predictive performance and uncertainty quantification. We introduce a method that automatically accounts for temporal misalignment in a unified generative model that improves predictive performance. Our method uses Gaussian processes (GPs) to model the correlations both within and between the tasks. Building on the previous work by Kazlauskaite et al. (2019), we include a separate monotonic warp of the input data to model temporal misalignment. In contrast to previous work, we formulate a lower bound that accounts for uncertainty in both the estimates of the warping process and the underlying functions. Also, our new take on a monotonic stochastic process, with efficient path-wise sampling for the warp functions, allows us to perform full Bayesian inference in the model rather than MAP estimates. Missing data experiments, on synthetic and real time-series, demonstrate the advantages of accounting for misalignments (vs standard unaligned method) as well as modelling the uncertainty in the warping process (vs baseline MAP alignment approach).
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| 10. |
- Sanders, Ella, et al.
(författare)
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The stabilization of S100A9 structure by calcium inhibits the formation of amyloid fibrils
- 2023
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Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 24:17
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Tidskriftsartikel (refereegranskat)abstract
- The calcium-binding protein S100A9 is recognized as an important component of the brain neuroinflammatory response to the onset and development of neurodegenerative disease. S100A9 is intrinsically amyloidogenic and in vivo co-aggregates with amyloid-β peptide and α-synuclein in Alzheimer’s and Parkinson’s diseases, respectively. It is widely accepted that calcium dyshomeostasis plays an important role in the onset and development of these diseases, and studies have shown that elevated levels of calcium limit the potential for S100A9 to adopt a fibrillar structure. The exact mechanism by which calcium exerts its influence on the aggregation process remains unclear. Here we demonstrate that despite S100A9 exhibiting α-helical secondary structure in the absence of calcium, the protein exhibits significant plasticity with interconversion between different conformational states occurring on the micro- to milli-second timescale. This plasticity allows the population of conformational states that favour the onset of fibril formation. Magic-angle spinning solid-state NMR studies of the resulting S100A9 fibrils reveal that the S100A9 adopts a single structurally well-defined rigid fibrillar core surrounded by a shell of approximately 15–20 mobile residues, a structure that persists even when fibrils are produced in the presence of calcium ions. These studies highlight how the dysregulation of metal ion concentrations can influence the conformational equilibria of this important neuroinflammatory protein to influence the rate and nature of the amyloid deposits formed.
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| 11. |
- Torsi, Luisa, et al.
(författare)
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Organic thin-film transistors for inorganic substance monitoring
- 2009. - 1
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Ingår i: Organic electronics in Sensors and Biotechnology. - New York : McGraw-Hill Companies Inc. - 9780071596756 ; , s. 51-91
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Develop high-performance, field-deployable organic semiconductor-based biological, chemical, and physical sensor arrays using the comprehensive information contained in this definitive volume. Organic Electronics in Sensors and Biotechnology presents state-of-the-art technology alongside real-world applications and ongoing R & D.Learn about light, temperature, and pressure monitors, integrated flexible pyroelectric sensors, sensing of organic and inorganic compounds, and design of compact photoluminescent sensors. You will also get full details on organic lasers, organic electronics in memory elements, disease and pathogen detection, and conjugated polymers for advancing cellular biology.Monitor organic and inorganic compounds with OFETsCharacterize organic materials using impedance spectroscopyWork with organic LEDs, photodetectors, and photovoltaic cellsForm flexible pyroelectric sensors integrated with OFETsBuild PL-based chemical and biological sensing modules and arraysDesign organic semiconductor lasers and memory elementsUse luminescent conjugated polymers as optical biosensorsDeploy polymer-based switches and ion pumps at the microfluidic level
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