| 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. |
- Lee, Amos C., et al.
(author)
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OPENchip : an on-chip in situ molecular profiling platform for gene expression analysis and oncogenic mutation detection in single circulating tumour cells
- 2020
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In: Lab on a Chip. - : Royal Society of Chemistry (RSC). - 1473-0197 .- 1473-0189. ; 20:5, s. 912-922
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Journal article (peer-reviewed)abstract
- Liquid biopsy holds promise towards practical implementation of personalized theranostics of cancer. In particular, circulating tumour cells (CTCs) can provide clinically actionable information that can be directly linked to prognosis or therapy decisions. In this study, gene expression patterns and genetic mutations in single CTCs are simultaneously analysed by strategically combining microfluidic technology and in situ molecular profiling technique. Towards this, the development and demonstration of the OPENchip (On-chip Post-processing ENabling chip) platform for single CTC analysis by epithelial CTC enrichment and subsequent in situ molecular profiling is reported. For in situ molecular profiling, padlock probes that identify specific desired targets to examine biomarkers of clinical relevance in cancer diagnostics were designed and used to create libraries of rolling circle amplification products. We characterize the OPENchip in terms of its capture efficiency and capture purity, and validate the probe design using different cell lines. By integrating the obtained results, molecular analyses of CTCs from metastatic breast cancer (HER2 (ERBB2) gene expression and PIK3CA mutations) and metastatic pancreatic cancer (KRAS gene mutations) patients were demonstrated without any off-chip processes. The results substantiate the potential implementation of early molecular detection of cancer through sequencing-free liquid biopsy.
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| 3. |
- Taylor, Simon J.E., et al.
(author)
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Using Simulation and Digital Twins to Innovate: Are we Getting Smarter?
- 2021
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In: Proceedings - Winter Simulation Conference. - 0891-7736. ; 2021-December
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Conference paper (peer-reviewed)abstract
- Digital Twins have recently emerged as a major new area of innovation. Digital Twins are often found at the core of 'smart' solutions that have also emerged as major areas of innovation. Modeling and Simulation (MS) approaches create a model of a real-world system that is linked to data sources and is used to simulate and predict the behavior of its real-world counterpart. On the face of it Digital Twins and MS appear to be similar, if not the same. Is this actually the case? Are the two fields really separate or is Digital Twin research re-inventing the 'MS wheel'? To investigate these relationships, in this panel we will explore some contemporary innovations with Digital Twins and discuss whether or not Digital Twins is a contemporary 'refresh' or 'rebranding' of MS or if there are exciting new synergies.
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