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Cells were exposed to either conditions of sterol depletion, defined as 24 hour incubation in media supplemented with 10% lipoprotein deficient serum (LPDS) and simvastatin (concentration varied by experiment), or sterol loading, defined as 24 hour incubation in media supplemented with 10% LPDS and either 50 µg/ml LDL-cholesterol or 1 µg/ml 25-hydroxycholesterol.
Since two patients included in our study showed no B cell depletion (defined as <5.0 B cells/mm) [ 41] and a poor clinical response to Rituximab, it is very likely that they bear this type of polymorphism.
Cartilage depletion, defined as the loss of proteoglycan content, was scored on a scale ranging from 0 to 3 per region, depending on the intensity of staining in the cartilage.
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Depletion: default defined Values.
Iron depletion was defined as low serum ferritin (SF<15 μg/l).
Significant fold enrichment or depletion was defined using hypergeometric distribution analysis (P-value < 0.001) combined with a fold change higher than 1.5 or smaller than 0.5, respectively.
The ferritin index, a measure of bone marrow iron depletion, was defined as soluble transferrin receptor/log ferritin (Punnonen et al., 1997).
Volume depletion was defined as a clinical situation resulting from decreased effective circulating volume and total extracellular fluid volume or as decreased effective circulating volume with increased total extracellular fluid volume.
A further problem in assessing BCDT is that successful depletion is defined by circulating total B-cell counts and this disregards the diversity of B-cell phenotype, function, and compartmentalization.
To test whether increased expression of C/EBPα was crucially involved in shifting the transcriptional network after RUNX1/ETO depletion, we defined overrepresented binding patterns for C/EBPα, PU.1, RUNX1, and LMO2 after RUNX1/ETO knockdown.
We checked the consistency of our assumption that the diffusive flux is rapid by verifying that the time scale for diffusion across the depletion depth, τ d = d/(2 D), is much smaller than the time scale for a sheet growing across the depletion depth, defined by L(t + τ g ) – L t) = 2 d.
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