| 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. |
- Kohantorabi, Mona, et al.
(författare)
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Light-Induced Transformation of Virus-Like Particles on TiO2
- 2024
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Ingår i: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 16:28, s. 37275-37287
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Tidskriftsartikel (refereegranskat)abstract
- Titanium dioxide (TiO2) shows significant potential as a self-cleaning material to inactivate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and prevent virus transmission. This study provides insights into the impact of UV-A light on the photocatalytic inactivation of adsorbed SARS-CoV-2 virus-like particles (VLPs) on a TiO2 surface at the molecular and atomic levels. X-ray photoelectron spectroscopy, combined with density functional theory calculations, reveals that spike proteins can adsorb on TiO2 predominantly via their amine and amide functional groups in their amino acids blocks. We employ atomic force microscopy and grazing-incidence small-angle X-ray scattering (GISAXS) to investigate the molecular-scale morphological changes during the inactivation of VLPs on TiO2 under light irradiation. Notably, in situ measurements reveal photoinduced morphological changes of VLPs, resulting in increased particle diameters. These results suggest that the denaturation of structural proteins induced by UV irradiation and oxidation of the virus structure through photocatalytic reactions can take place on the TiO2 surface. The in situ GISAXS measurements under an N2 atmosphere reveal that the virus morphology remains intact under UV light. This provides evidence that the presence of both oxygen and UV light is necessary to initiate photocatalytic reactions on the surface and subsequently inactivate the adsorbed viruses. The chemical insights into the virus inactivation process obtained in this study contribute significantly to the development of solid materials for the inactivation of enveloped viruses.
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| 4. |
- Schael, S, et al.
(författare)
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Precision electroweak measurements on the Z resonance
- 2006
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Ingår i: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Forskningsöversikt (refereegranskat)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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| 5. |
- Schuette, Moritz, et al.
(författare)
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Molecular dissection of colorectal cancer in pre-clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors
- 2017
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Colorectal carcinoma represents a heterogeneous entity, with only a fraction of the tumours responding to available therapies, requiring a better molecular understanding of the disease in precision oncology. To address this challenge, the OncoTrack consortium recruited 106 CRC patients (stages I-IV) and developed a pre-clinical platform generating a compendium of drug sensitivity data totalling 44,000 assays testing 16 clinical drugs on patient-derived in vivo and in vitro models. This large biobank of 106 tumours, 35 organoids and 59 xenografts, with extensive omics data comparing donor tumours and derived models provides a resource for advancing our understanding of CRC. Models recapitulate many of the genetic and transcriptomic features of the donors, but defined less complex molecular sub-groups because of the loss of human stroma. Linking molecular profiles with drug sensitivity patterns identifies novel biomarkers, including a signature outperforming RAS/RAF mutations in predicting sensitivity to the EGFR inhibitor cetuximab.
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| 6. |
- Butorin, Sergei, et al.
(författare)
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Effect of carbon content on electronic structure of uranium carbides
- 2023
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure of UCx (x = 0.9, 1.0, 1.1, 2.0) was studied by means of x-ray absorption spectroscopy (XAS) at the CK edge and measurements in the high energy resolution fluorescence detection (HERFD) mode at the U M-4 and L-3 edges. The full-relativistic density functional theory calculations taking into account the 5f - 5f Coulomb interaction U and spin-orbit coupling (DFT+U+SOC) were also performed for UCand UC2. While the U L-3 HERFD-XAS spectra of the studied samples reveal little difference, the U M-4 HERFD-XAS spectra show certain sensitivity to the varying carbon content in uranium carbides. The observed gradual changes in the U M-4 HERFD spectra suggest an increase in the C2p-U 5f charge transfer, which is supported by the orbital population analysis in the DFT+U+ SOC calculations, indicating an increase in the U 5f occupancy in UC2 as compared to that in UC. On the other hand, the density of states at the Fermi level were found to be significantly lower in UC2, thus affecting the thermodynamic properties. Both the x-ray spectroscopic data (in particular, the CK XAS measurements) and results of the DFT+U+SOC calculations indicate the importance of taking into account U and SOC for the description of the electronic structure of actinide carbides.
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| 7. |
- Butorin, Sergei, et al.
(författare)
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X-ray spectroscopic study of chemical state in uranium carbides
- 2022
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Ingår i: Journal of Synchrotron Radiation. - : International Union of Crystallography (IUCr). - 0909-0495 .- 1600-5775. ; 29, s. 295-302
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Tidskriftsartikel (refereegranskat)abstract
- UC and UMeC2 (Me = Fe, Zr, Mo) carbides were studied by the high-energyresolution fluorescence-detected X-ray absorption (HERFD-XAS) technique at the U M-4 and L-3 edges. Both U M-4 and L-3 HERFD-XAS reveal some differences between UMeC2 and UC; there are differences also between the M-4 and L-3 edge results for both types of carbide in terms of the spectral width and energy position. The observed differences are attributed to the consequences of the U 5f, 6d-4d(3d) hybridization in UMeC2. Calculations of the U M-4 HERFD-XAS spectra were also performed using the Anderson impurity model (AIM). Based on the analysis of the data, the 5f occupancy in the ground state of UC was estimated to be 3.05 electrons. This finding is also supported by the analysis of U N-4,N-5 XAS of UC and by the results of the AIM calculations of the U 4f X-ray photoelectron spectrum of UC.
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| 8. |
- Mardor, Israel, et al.
(författare)
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Determining spontaneous fission properties by direct mass measurements with the FRS Ion Catcher
- 2020
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Ingår i: ND 2019. - : EDP Sciences. - 9782759891061
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Konferensbidrag (refereegranskat)abstract
- We present a direct method to measure fission product yield distributions (FPY) and isomeric yield ratios (IYR) for spontaneous fission (SF) fragments. These physical properties are of utmost importance to the understanding of basic nuclear physics, the astrophysical rapid neutron capture process ('r process') of nucle-osynthesis, neutron star composition, and nuclear reactor safety. With this method, fission fragments are produced by spontaneous fission from a source that is mounted in a cryogenic stopping cell (CSC), thermalized and stopped within it, and then extracted and transported to a multiple-reflection time-of-flight mass-spectrometer (MR-TOF-MS). We will implement the method at the FRS Ion Catcher (FRS-IC) at GSI (Germany), whose MR-TOF-MS relative mass accuracy (similar to 10(-7)) and resolving power (similar to 600,000 FWHM) are sufficient to separate all isobars and numerous isomers in the fission fragment realm. The system's essential element independence and its fast simultaneous mass measurement provide a new direct way to measure isotopic FPY distributions, which is complementary to existing methods. It will enable nuclide FPY measurements in the high fission peak, which is hardly accessible by current techniques. The extraction time of the CSC, tens of milliseconds, enables a direct measurement of independent fission yields, and a first study of the temporal dependence of FPY distributions in this duration range. The ability to resolve isomers will further enable direct extraction of numerous IYRs while performing the FPY measurements. The method has been recently demonstrated at the FRS-ICr for SF with a 37 kBq Cf-252 fission source, where about 70 different fission fragments have been identified and counted. In the near future, it will be used for systematic studies of SF with a higher-activity Cf-252 source and a Cm-248 source. The method can be implemented also for neutron induced fission at appropriate facilities.
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| 9. |
- Waschitz, Y., et al.
(författare)
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Independent isotopic fission yields of Cf-252 spontaneous fission via mass measurements at the FRS Ion Catcher
- 2023
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Ingår i: 15th International Conference on Nuclear Data for Science and Technology, ND2022. - : EDP Sciences.
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Konferensbidrag (refereegranskat)abstract
- We present first preliminary results of a novel method for measuring independent isotopic fission yields (IIFYs) of spontaneous fission (SF) via direct mass measurements, at the FRS Ion Catcher (FRS -IC) at GSI. Fission products were generated from a Cf-252 source installed in a cryogenic stopping cell, and were identified and counted with the multiple-reflection time-of-flight mass spectrometer (MR-TOR-MS) of the FRS-IC, utilizing well-established measurement and data analysis methods. The MR-TOR-MS resolves isobars unambiguously, even with limited statistics, and its non-scanning nature ensures minimal relative systematic uncertainties amongst fission products. The analysis for extracting IIFYs includes isotope-dependent efficiency corrections for all components of the FRS -IC. In particular, we applied a self-consistent technique that takes into account the element-dependent survival efficiencies in the CSC, due to chemical reactions with the buffer gas. Our IIFY results, which cover several tens of fission products in the less -accessible high-mass peak (Z = 56 to 63) down to fission yields at the level of 10(-5), are generally similar to those of the nuclear database ENDF/B-VII.O. Nevertheless, they reveal some structures that are not observed in the database smooth trends. These are the first results of a planned campaign to investigate IIFY distributions of spontaneous fission at the FRS-IC. Upcoming experiments will extend our results to wider Z and N ranges, lower fission yields, and other spontaneously-fissioning actinides.
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