| 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. |
- Noreen, Khadija, et al.
(författare)
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Algorithms to obtain generalized neighbor designs in minimal circular blocks
- 2022
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Ingår i: Communications in statistics. Simulation and computation. - : Taylor & Francis. - 0361-0918 .- 1532-4141.
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Tidskriftsartikel (refereegranskat)abstract
- The experiments where response of a treatment (direct effect) is affected by the treatment(s) applied in neighboring units, neighbor designs are used to balance the neighbor effects. Being the economical, minimal neighbor designs are preferred by the experimenters. Minimal circular neighbor designs could not be constructed for almost every case of v even, where v is number of treatments. For v even, minimal circular generalized neighbor designs are preferred. In this article, algorithms are developed to obtain minimal circular generalized neighbor designs in which (a) v/2 of the unordered pairs, and (b) 3v/2 of the unordered pairs, do not appear as neighbor whereas the remaining ones appear once. These algorithms are also coded with R-language.
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| 3. |
- Fardos, Akbar, et al.
(författare)
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Algorithm to generate efficient circular designs robust to neighbor effects
- 2024
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Ingår i: Kuwait Journal of Science. - 2307-4108. ; 51:1
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Tidskriftsartikel (refereegranskat)abstract
- Minimal circular balanced and strongly balanced neighbor designs (MCBNDs & MCSBNDs) are popular to control neighbor effects and to estimate neighbor and direct effects independently. In this article, an R-coded algorithm is presented to obtain efficient MCBNDs and MCSBNDs for odd v (number of treatments), and its four generalized classes for v even. Developed algorithm has made the construction of the efficient circular designs robust to neighbor effects so easy in blocks of equal and unequal sizes.
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| 4. |
- Hassan, Jamshaidul, et al.
(författare)
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Construction of circular quasi rees neighbor designs which can be converted into minimal circular balanced and strongly balanced neighbor designs
- 2023
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Ingår i: Communications in Statistics - Theory and Methods. - : Informa UK Limited. - 0361-0926 .- 1532-415X. ; 52:16, s. 5587-5605
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Tidskriftsartikel (refereegranskat)abstract
- The response of a treatment (direct effect) applied on a given unit may be affected by the treatments applied to its neighboring units (neighbor effects). Neighbor designs are considered robust to neighbor effects. Minimal neighbor designs are economical, therefore, these are preferred by the experimenters. Method of cyclic shifts (Rule I) provides the minimal neighbor designs for odd v (number of treatments). Method of cyclic shifts (Rule II) provides the minimal circular Quasi Rees neighbor designs for v even which are considered to be the good alternate to the minimal neighbor designs. In this article, for every case of v even, minimal circular Quasi Rees neighbor designs are constructed in such a way that these designs can also be converted directly into minimal circular balanced and strongly balanced neighbor designs.
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| 5. |
- Nadeem, Muhammad, et al.
(författare)
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New generators for minimal circular generalised neighbour designs in blocks of two different sizes
- 2023
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Ingår i: Statistics in Transition New Series. - 1234-7655 .- 2450-0291. ; 24:2, s. 85-92
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Tidskriftsartikel (refereegranskat)abstract
- Minimal neighbour designs (NDs) are used when a response of a treatment (direct effect) is affected by the treatment(s) applied in the neighbouring units. Minimal generalised NDs are preferred when minimal NDs cannot be constructed. Through the method of cyclic shifts (Rule I), the conditions for the existence of minimal circular generalised NDs are discussed, in which v/2 unordered pairs do not appear as neighbours. Certain generators are also developed to obtain minimal circular generalised NDs in blocks of two different sizes, where k2 = 3, 4 and 5. All these designs are constructed using i sets of shifts for k1 and two for k2.
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| 6. |
- Noreen, Khadija, et al.
(författare)
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Some important classes of non-directional minimal circular weakly balanced neighbor designs
- 2023
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Ingår i: Communications in statistics. Simulation and computation. - 0361-0918 .- 1532-4141. ; , s. 1-10
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Tidskriftsartikel (refereegranskat)abstract
- Minimal neighbor designs are useful to balance out neighbor effects economically. The method of cyclic shifts provides the construction of these minimal designs in circular blocks only for v odd, where v is the number of treatments to be compared. Minimal circular weakly balanced neighbor designs are used for v even. In this article, two classes of minimal circular weakly balanced neighbor designs are constructed for v even. In class I, v/2 of all unordered pairs of two distinct treatments appear twice as neighbors while the remaining ones appear once. In class II, 3v/2 of all unordered pairs appear twice as neighbors.
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| 7. |
- Rasheed, H. M. Kashif, et al.
(författare)
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Efficient circular repeated measurements designs strongly balanced to control carryover effects
- 2024
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Ingår i: Communications in statistics. Simulation and computation. - 0361-0918 .- 1532-4141.
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Tidskriftsartikel (refereegranskat)abstract
- In experiments related to agriculture, psychology, medicine, animal sciences, pharmacology, and other fields, repeated measurements designs (RMDs) are utilized which are economical design. However, the use of these designs may result in carryover effects, which are the primary cause of bias. Balanced or strongly balanced RMDs can control these effects. Strongly balanced RMDs estimate the direct effects and carryover effects independently; therefore, these designs have an edge over the balanced RMDs. In this article, therefore, some general procedures are presented to obtain minimal circular strongly and nearly strongly balanced RMDs in periods of k different sizes with high efficiency of Separability and of carryover effects.
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