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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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| 2. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 3. |
- Yang, Xia, et al.
(författare)
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Integrated assessment of indoor and outdoor ventilation in street canyons with naturally-ventilated buildings by various ventilation indexes
- 2020
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 169
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Tidskriftsartikel (refereegranskat)abstract
- The integrated assessments of indoor and outdoor ventilation are still rare so far. As a novelty, this paper aims to quantify the influence of street aspect ratios (building height/street width, H/W = 0.5–5) and window sizes (1 m × 1 m, 1.5 m × 1.5 m) on indoor-outdoor ventilation in two-dimensional streets with single-sided naturally-ventilated buildings. Numerical simulations with RNG k-ε model are validated against experimental data and the grid independence are tested as well. Air change rates per hour (ACH, h−1) are adopted for assessing indoor-outdoor ventilation by mean flows (ACHmean) and turbulent fluctuations (ACHturb) respectively. Age of air(τ), purging flow rate (PFR) and its corresponding ACHPFR are used to evaluate overall ventilation capacities.Shallower streets experience better indoor-outdoor ventilation. Outdoor ACHPFR drop from 14.69 to 17.55 h−1 to 3.96–3.97 h−1 as H/W rises from 0.5 to 3. In extremely deep canyon (H/W = 5), two-counter-rotating vortices produce much smaller velocity at low-level regions (U/Uref~10−3-10−5), resulting in small ACHPFR for outdoor (~0.76–0.91 h−1) and indoor in 1–13th floors (~0.03–0.61 h−1). When H/W = 0.5–1, leeward 5–6th floors experience smaller ACHPFR(e.g.~1.13–1.40 h−1 as H/W = 1) than the other floors (e.g. ~1.54–9.52 h−1 as H/W = 1). Particularly, as H/W = 2–3, leeward-side indoor ACHPFR in the middle floors (except the first and top two floors) are nearly constants (~1.02–1.69 h−1) and much smaller than windward-side ACHPFR(~1.41–4.35 h−1) which increase toward upper floors. Besides, the smaller window size reduces indoor ACHPFR by 19.38%~88.28%, but hardly influences outdoor ventilation. Moreover, both outdoor and indoor ACHPFR are greater than ACHmean but smaller than ACHmean + ACHturb. Although further investigations are still required, this paper provides an insight and scientific foundation on integrated indoor-outdoor ventilation evaluation with various effective ventilation indexes.
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