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The results are exceptionally clear and in full agreement with the superimposed structures shown in the right panel of Fig. 1: The native simulation is fully biased towards the α-helical state and fails to reproduce the experimentally observed 310 helix (this can also be inferred by comparing the structures depicted in Fig. 1).
We argue that this may not be the case, exactly because the forcefield is biased: A forcefield fully biased towards a folded helical state can only damp (underestimate) the destabilizing effects of mutations/deletions, especially when these mutations/deletions correspond to structurally disordered residues as judged by this same forcefield.
When all trials are similarly biased, the DTC and the inconsistency Bayesian MTC (RIBMTC) are fully biased, while the AITC is not biased.
The blue curves in Figure 5 indicated that structural changes in the T monomer were significant but not as large as those observed in the fully biased simulations.
The blue curves in Figure 5 indicated that structural changes in the T monomer were not as large as those observed in the fully biased simulations but had the same trend.
The impacts of biases in primary studies on the validity of different comparison methods are summarised in Table 2. (Note: "Fully biased" – the bias equals the bias in trials; "Moderately biased" – as a result of combining biased direct estimate and unbiased indirect estimate, or a result of combining unbiased direct estimate and biased indirect estimate).
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The discrepancy may be due to the fact that the stimuli used by [9] were not fully ambiguous but biased toward one interpretation.
We also showed that selection of all sequenced bacteria as a reference genome set may not produce the optimal PPV since the set of fully sequenced bacteria is biased towards pathogens and laboratory species (i.e. E. coli) among others.
Arguably, one of the most significant problems – certainly the one that generates most friction – is that reviewers can safely dispense self-serving and biased critiques, fully protected by the mask of anonymity.
Our use of other diabetes medications as comparators, however, should reduce or eliminate the majority of these potential biases, although we cannot fully exclude biases introduced by physicians or patients leading to selection of specific drugs.
Similarly, in elderly women, some ovarian cancers are not fully investigated, which biases their incidence [ 26].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com