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Two potential problems with this study are 1) the stimulus set was restricted to just planar surfaces, which are a very small subset of possible 3D shapes; and 2) no 2D controls were provided to show that subjects were not using 2D properties, such as the position of the coarsest dots or the orientation of the dot alignments in order to perform the slant judgments.
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That said, the dot alignment from the simulations is similar to that seen in the growth experiments on Si0.25Ge0.75 QDs discussed by Tersoff et al. [14, 24].
The spin quantization axis (z-axis) is chosen along direction [100] (Figure 1a) and 2D dot distribution is random; (ii) Correlated dots, which consider anisotropic spatial confinement ( D [ 011 ] ≠ D [ 0 1 ¯ 1 ] ) and include inter-dot coupling (Figure 1b) that leads to a chain-like 1D dot alignment.
Model means are plotted in Figure 3. Since dot alignment was not significant, a single regression line has been fitted to the average of the two conditions.
The dot plot alignments were generated using the MUMmer package [37] (http://mummer.sourceforge.net/).net/
Further, note that two perfect dot plot alignments can still have different quality when analyzed with the FRC.
The potato-tomato dot plot alignments explained the discrepancies that were found between the potato and tomato genetic maps.
Dot plot alignments were generated using the EMBOSS dottup program (Rice et al. 2000) with window size = 9 and step size = 1.
The dot plot alignments to tomato made useful suggestions on how to place as yet unordered potato superscaffolds and superscaffold blocks, after which nearly always BAC end sequence links were identified in potato that confirmed the suggested orientation.
Included in the refinement process were dot plot alignments of DM chromosome PM sequences to pre-release and finished versions of the tomato genome sequence (The Tomato Genome Sequencing Consortium 2012).
Dot plot alignment of the CG14 and Nipponbare orthologous sequences around genes 88O22.2/88O22.7 evidenced a paracentric chromosomal inversion of approximately 45 kb (Figure 3, box D).
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