Conditioned spin and charge dynamics of a single electron quantum dot

In this article we describe the incoherent and coherent spin and charge dynamics of a single electron quantum dot. We use a stochastic master equation to model the state of the system, as inferred by an observer with access to only the measurement signal. Measurements obtained during an interval of time contribute, by a past quantum state analysis, to our knowledge about the system at any time $t$ within that interval. Such analysis permits precise estimation of physical parameters, and we propose and test a modification of the classical Baum-Welch parameter re-estimation method to systems driven by both coherent and incoherent processes.Comment: 9 pages, 9 figure

Additional file 1: Figure S1. of Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Clinical trial BR9601 information. (a) Schematic representation. (b) Patient information. Figure S2. Entire FI network from 61 consistently changing genes. Red circles = upregulated genes; green circles = downregulated genes; diamonds = linker genes. Figure S3. Heat maps of probes for the 61 consistently changing genes. Rows are labelled with gene symbol and microarray probe IDs. (a) Raw expression values. (b) Row scaled expression values. Figure S4. Combination of pre-processing methods. The most optimal method selected was at the top(high-rank). Figure S5. Sample-by-gene heat map. Rows represent patients and columns represent genes. Both were clustered using a ward clustering algorithm. Figure S6. FI network generated from the histone module. Circles = genes within the module, diamonds = linker genes. Figure S7. Multiplot showing scaled mRNA abundance levels for each gene. A treatment-by-marker interaction Cox proportional hazards model was fit for each gene, and results are visualized on the right with the squares representing the hazard ratios (HRs) and the ends of the segments representing the 95 % confidence intervals in log2 scale. Patients are sorted by DRFS events on the x-axis and genes by decreasing log2 HR on the y-axis. Figure S8. Flow cytometric analysis of HER2 in MCF7 cells. Yellow dotted line represents HER2- cell line (MDA-MB-231), while purple dotted line shows HER2 amplified cell line (SKBR3). Green and blue solid lines represent native and epirubicin-resistant MCF7 cell lines, respectively, and show they are negative for HER2 cell surface expression. Table S1. Doubling times (in hours) of breast cancer cell lines. Table S2 List of 61 common genes with consistent differential expression across all four cell lines. Table S3. Percentage reduction in gene expression compared with non-targeting siRNA control. Table S4. Drugs targeting epirubicin-resistant breast cancer cells. Table S5. List of primary antibodies. Table S6. List of histone module genes in the NanoString CodeSet. (PDF 1653 kb

Additional file 2: of Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer

Description of mRNA abundance data processing, module dysregulation score (MDS) and survival modelling. (PDF 360 kb