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- Diederichs, J., et al.
(author)
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Critical currents in Tl-2122 and Y-124 sinters under high hydrostatic pressure
- 1991
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In: Superconductor Science and Technology, volume 4, Special Issue 1S. - Bristol : Adam Hilger. - 0750301082 ; , s. S97-S99
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Conference paper (peer-reviewed)abstract
- Utilizing AC susceptibility measurements the authors have investigated the inter and intragranular properties of selected bulk materials under hydrostatic pressures to 3.5 GPa. A single phase Tl2CaBa2Cu2O8 sample with superconducting transition temperature Tc approximately=107 K shows a clear maximum in Tc(P) at approximately 2.2 GPa coupled with a nearly twofold increase to 3 GPa of the intergranular critical current density JcJ near Tc. The second sample, a YBa2Cu4O8 sinter, shows a large linear increase in Tc with pressure (+5.5 K/GPa) as well as a fivefold increase JcJ to 3 GPa. Applying a critical state model, the authors find that Tc(P) varies as lambda g-2(P), where lambda g is the intragranular (London) penetration depth.
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| 2. |
- Murina, Victoriia, et al.
(author)
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ABCF ATPases Involved in Protein Synthesis, Ribosome Assembly and Antibiotic Resistance : Structural and Functional Diversification across the Tree of Life
- 2019
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In: Journal of Molecular Biology. - : Elsevier. - 0022-2836 .- 1089-8638. ; 431:18, s. 3568-3590
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Journal article (peer-reviewed)abstract
- Within the larger ABC superfamily of ATPases, ABCF family members eEF3 in Saccharomyces cerevisiae and EttA in Escherichia coli have been found to function as ribosomal translation factors. Several other ABCFs including biochemically characterized VgaA, LsaA and MsrE confer resistance to antibiotics that target the peptidyl transferase center and exit tunnel of the ribosome. However, the diversity of ABCF subfamilies, the relationships among subfamilies and the evolution of antibiotic resistance (ARE) factors from other ABCFs have not been explored. To address this, we analyzed the presence of ABCFs and their domain architectures in 4505 genomes across the tree of life. We find 45 distinct subfamilies of ABCFs that are widespread across bacterial and eukaryotic phyla, suggesting that they were present in the last common ancestor of both. Surprisingly, currently known ARE ABCFs are not confined to a distinct lineage of the ABCF family tree, suggesting that ARE can readily evolve from other ABCF functions. Our data suggest that there are a number of previously unidentified ARE ABCFs in antibiotic producers and important human pathogens. We also find that ATPase-deficient mutants of all four E. coli ABCFs (EttA, YbiT, YheS and Uup) inhibit protein synthesis, indicative of their ribosomal function, and demonstrate a genetic interaction of ABCFs Uup and YheS with translational GTPase BipA involved in assembly of the 50S ribosome subunit. Finally, we show that the ribosome-binding resistance factor VmlR from Bacillus subtilis is localized to the cytoplasm, ruling out a role in antibiotic efflux.
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| 3. |
- Persson, Sebastian, et al.
(author)
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PEPSDI: Scalable and flexible inference framework for stochastic dynamic single-cell models
- 2021
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Other publication (other academic/artistic)abstract
- Mathematical modelling is an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic and extrinsic noise. Here we present PEPSDI, a scalable and flexible framework for Bayesian inference in state-space mixed-effects stochastic dynamic single-cell models. Unlike previous frameworks, PEPSDI imposes a few modelling assumptions when inferring unknown model parameters from time-lapse data. Specifically, it can infer model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. This allowed us to identify hexokinase activity as a source of extrinsic noise, and to deduce that sugar availability dictates cell-to-cell variability in the budding yeast Saccharomyces cerevisiae SNF1 nutrient sensing pathway.
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| 4. |
- Persson, Sebastian, 1996, et al.
(author)
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Scalable and flexible inference framework for stochastic dynamic single-cell models
- 2022
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In: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 18
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Journal article (peer-reviewed)abstract
- Understanding the inherited nature of how biological processes dynamically change over time and exhibit intra- and inter-individual variability, due to the different responses to environmental stimuli and when interacting with other processes, has been a major focus of systems biology. The rise of single-cell fluorescent microscopy has enabled the study of those phenomena. The analysis of single-cell data with mechanistic models offers an invaluable tool to describe dynamic cellular processes and to rationalise cell-to-cell variability within the population. However, extracting mechanistic information from single-cell data has proven difficult. This requires statistical methods to infer unknown model parameters from dynamic, multi-individual data accounting for heterogeneity caused by both intrinsic (e.g. variations in chemical reactions) and extrinsic (e.g. variability in protein concentrations) noise. Although several inference methods exist, the availability of efficient, general and accessible methods that facilitate modelling of single-cell data, remains lacking. Here we present a scalable and flexible framework for Bayesian inference in state-space mixed-effects single-cell models with stochastic dynamic. Our approach infers model parameters when intrinsic noise is modelled by either exact or approximate stochastic simulators, and when extrinsic noise is modelled by either time-varying, or time-constant parameters that vary between cells. We demonstrate the relevance of our approach by studying how cell-to-cell variation in carbon source utilisation affects heterogeneity in the budding yeast Saccharomyces cerevisiae SNF1 nutrient sensing pathway. We identify hexokinase activity as a source of extrinsic noise and deduce that sugar availability dictates cell-to-cell variability.
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