Graphical technique for identifying a monotonic variance stabilizing transformation for absolute gene intensity signals

BACKGROUND: The usefulness of log(2 )transformation for cDNA microarray data has led to its widespread application to Affymetrix data. For Affymetrix data, where absolute intensities are indicative of number of transcripts, there is a systematic relationship between variance and magnitude of measurements. Application of the log(2 )transformation expands the scale of genes with low intensities while compressing the scale of genes with higher intensities thus reversing the mean by variance relationship. The usefulness of these transformations needs to be examined. RESULTS: Using an Affymetrix GeneChip(® )dataset, problems associated with applying the log(2 )transformation to absolute intensity data are demonstrated. Use of the spread-versus-level plot to identify an appropriate variance stabilizing transformation is presented. For the data presented, the spread-versus-level plot identified a power transformation that successfully stabilized the variance of probe set summaries. CONCLUSION: The spread-versus-level plot is helpful to identify transformations for variance stabilization. This is robust against outliers and avoids assumption of models and maximizations

A Mechatronic Approach to Control of 6 DOF Parallel Manipulator

This paper presents a practical implementation, using reconfigurable computing applied to robotic problems. Through the proposal a hierarchical architecture, distributing the several control actions in growing levels of complexity and using resources of reconfigurable computing is possible to take into account the easiness of future modifications, updates and improvements in the robotic applications. A practical example is presenting using reconfigurable computing, of Stewart- Gough platform control, where the developed software and hardware are structured in independent blocks, through open architecture implementation, allowing the easy expansion of the system, better adapting the platform to the tasks associated to it. This open architecture implementation allows an easy expansion of the system and a better adaptation of the platform to its related tasks.N/

Kerr non-linearity in a superconducting Josephson metamaterial

We present a detailed experimental and theoretical analysis of the dispersion and non-linear Kerr frequency shifts of plasma modes in a one-dimensional Josephson junction chain containing 500 SQUIDs in the regime of weak nonlinearity. The measured low-power dispersion curve agrees perfectly with the theoretical model if we take into account the Kerr renormalisation of the bare frequencies and the long-range nature of the island charge screening by a remote ground plane. We measured the self- and cross-Kerr shifts for the frequencies of the eight lowest modes in the chain. We compare the measured Kerr coefficients with theory and find good agreement

Kerr coefficients of plasma resonances in Josephson junction chains

We present an experimental and theoretical analysis of the self- and cross-Kerr effect of extended plasma resonances in Josephson junction chains. We calculate the Kerr coefficients by deriving and diagonalizing the Hamiltonian of a linear circuit model for the chain and then adding the Josephson non-linearity as a perturbation. The calculated Kerr-coefficients are compared with the measurement data of a chain of 200 junctions. The Kerr effect manifests itself as a frequency shift that depends linearly on the number of photons in a resonant mode. By changing the input power on a low signal level, we are able to measure this shift. The photon number is calibrated using the self-Kerr shift calculated from the sample parameters. We then compare the measured cross-Kerr shift with the theoretical prediction, using the calibrated photon number.Comment: 10 pages, 9 figure

Fast high fidelity quantum non-demolition qubit readout via a non-perturbative cross-Kerr coupling

Qubit readout is an indispensable element of any quantum information processor. In this work, we experimentally demonstrate a non-perturbative cross-Kerr coupling between a transmon and a polariton mode which enables an improved quantum non-demolition (QND) readout for superconducting qubits. The new mechanism uses the same experimental techniques as the standard QND qubit readout in the dispersive approximation, but due to its non-perturbative nature, it maximizes the speed, the single-shot fidelity and the QND properties of the readout. In addition, it minimizes the effect of unwanted decay channels such as the Purcell effect. We observed a single-shot readout fidelity of 97.4% for short 50 ns pulses, and we quantified a QND-ness of 99% for long measurement pulses with repeated single-shot readouts

Comparison of Effects of p53 Null and Gain-of-Function Mutations on Salivary Tumors in MMTV-Hras Transgenic Mice

p53 is an important tumor suppressor gene which is mutated in ~50% of all human cancers. Some of these mutants appear to have acquired novel functions beyond merely losing wild-type functions. To investigate these gain-of-function effects in vivo, we generated mice of three different genotypes: MMTV-Hras/p53+/+, MMTV-Hras/p53-/-, and MMTV-Hras/p53R172H/R172H. Salivary tumors from these mice were characterized with regard to age of tumor onset, tumor growth rates, cell cycle distribution, apoptotic levels, tumor histopathology, as well as response to doxorubicin treatment. Microarray analysis was also performed to profile gene expression. The MMTV-Hras/p53-/- and MMTV-Hras/p53R172H/R172H mice displayed similar properties with regard to age of tumor onset, tumor growth rates, tumor histopathology, and response to doxorubicin, while both groups were clearly distinct from the MMTV-Hras/p53+/+ mice by these measurements. In addition, the gene expression profiles of the MMTV-Hras/p53-/- and MMTV-Hras/p53R172H/R172H tumors were tightly clustered, and clearly distinct from the profiles of the MMTV-Hras/p53+/+ tumors. Only a small group of genes showing differential expression between the MMTV-Hras/p53-/- and MMTV-Hras/p53R172H/R172H tumors, that did not appear to be regulated by wild-type p53, were identified. Taken together, these results indicate that in this MMTV-Hras-driven salivary tumor model, the major effect of the p53 R172H mutant is due to the loss of wild-type p53 function, with little or no gain-of-function effect on tumorigenesis, which may be explained by the tissue- and tumor type-specific properties of this gain-of-function mutant of p53