| 1. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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. |
- Gisselsson Nord, David, et al.
(author)
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When the genome plays dice: circumvention of the spindle assembly checkpoint and near-random chromosome segregation in multipolar cancer cell mitoses.
- 2008
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 3:4
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Journal article (peer-reviewed)abstract
- BACKGROUND: Normal cell division is coordinated by a bipolar mitotic spindle, ensuring symmetrical segregation of chromosomes. Cancer cells, however, occasionally divide into three or more directions. Such multipolar mitoses have been proposed to generate genetic diversity and thereby contribute to clonal evolution. However, this notion has been little validated experimentally. PRINCIPAL FINDINGS: Chromosome segregation and DNA content in daughter cells from multipolar mitoses were assessed by multiphoton cross sectioning and fluorescence in situ hybridization in cancer cells and non-neoplastic transformed cells. The DNA distribution resulting from multipolar cell division was found to be highly variable, with frequent nullisomies in the daughter cells. Time-lapse imaging of H2B/GFP-labelled multipolar mitoses revealed that the time from the initiation of metaphase to the beginning of anaphase was prolonged and that the metaphase plates often switched polarity several times before metaphase-anaphase transition. The multipolar metaphase-anaphase transition was accompanied by a normal reduction of cellular cyclin B levels, but typically occurred before completion of the normal separase activity cycle. Centromeric AURKB and MAD2 foci were observed frequently to remain on the centromeres of multipolar ana-telophase chromosomes, indicating that multipolar mitoses were able to circumvent the spindle assembly checkpoint with some sister chromatids remaining unseparated after anaphase. Accordingly, scoring the distribution of individual chromosomes in multipolar daughter nuclei revealed a high frequency of nondisjunction events, resulting in a near-binomial allotment of sister chromatids to the daughter cells. CONCLUSION: The capability of multipolar mitoses to circumvent the spindle assembly checkpoint system typically results in a near-random distribution of chromosomes to daughter cells. Spindle multipolarity could thus be a highly efficient generator of genetically diverse minority clones in transformed cell populations.
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| 3. |
- Kriegner, Dominik, et al.
(author)
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Ferroelectric phase transitions in multiferroic Ge1-xMnxTe driven by local lattice distortions
- 2016
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In: PHYSICAL REVIEW B. - 2469-9950. ; 94:5
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Journal article (peer-reviewed)abstract
- The evolution of local ferroelectric lattice distortions in multiferroic Ge1-xMnxTe is studied by x-ray diffraction, x-ray absorption spectroscopy, and density functional theory. We show that the anion/cation displacements smoothly decrease with increasing Mn content, thereby reducing the ferroelectric transition from 700 to 100 K at x = 0.5, where the ferromagnetic Curie temperature reaches its maximum. First principles calculations explain this quenching by different local bond contributions of the Mn 3d shell compared to the Ge 4s shell in excellent quantitative agreement with the experiments.
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| 4. |
- Menkveld, Albert J., et al.
(author)
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Nonstandard Errors
- 2024
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In: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Journal article (peer-reviewed)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 5. |
- Townend, Paul, et al.
(author)
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COGNIT: challenges and vision for a serverless and multi-provider cognitive cloud-edge continuum
- 2023
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In: 2023 IEEE International Conference on Edge Computing and Communications (EDGE). - : IEEE. - 9798350304831 - 9798350304848 ; , s. 12-22
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Conference paper (peer-reviewed)abstract
- Use of the serverless paradigm in cloud application development is growing rapidly, primarily driven by its promise to free developers from the responsibility of provisioning, operating, and scaling the underlying infrastructure. However, modern cloud-edge infrastructures are characterized by large numbers of disparate providers, constrained resource devices, platform heterogeneity, infrastructural dynamicity, and the need to orchestrate geographically distributed nodes and devices over public networks. This presents significant management complexity that must be addressed if serverless technologies are to be used in production systems. This position paper introduces COGNIT, a major new European initiative aiming to integrate AI technology into cloud-edge management systems to create a Cognitive Cloud reference framework and associated tools for serverless computing at the edge. COGNIT aims to: 1) support an innovative new serverless paradigm for edge application management and enhanced digital sovereignty for users and developers; 2) enable on-demand deployment of large-scale, highly distributed and self-adaptive serverless environments using existing cloud resources; 3) optimize data placement according to changes in energy efficiency heuristics and application demands and behavior; 4) enable secure and trusted execution of serverless runtimes. We identify and discuss seven research challenges related to the integration of serverless technologies with multi-provider Edge infrastructures and present our vision for how these challenges can be solved. We introduce a high-level view of our reference architecture for serverless cloud-edge continuum systems, and detail four motivating real-world use cases that will be used for validation, drawing from domains within Smart Cities, Agriculture and Environment, Energy, and Cybersecurity.
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