curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

This article introduces a manually curated data collection for gene expression meta-analysis of patients with ovarian cancer and software for reproducible preparation of similar databases. This resource provides uniformly prepared microarray data for 2970 patients from 23 studies with curated and documented clinical metadata. It allows users to efficiently identify studies and patient subgroups of interest for analysis and to perform meta-analysis immediately without the challenges posed by harmonizing heterogeneous microarray technologies, study designs, expression data processing methods and clinical data formats. We confirm that the recently proposed biomarker CXCL12 is associated with patient survival, independently of stage and optimal surgical debulking, which was possible only through meta-analysis owing to insufficient sample sizes of the individual studies. The database is implemented as the curatedOvarianData Bioconductor package for the R statistical computing language, providing a comprehensive and flexible resource for clinically oriented investigation of the ovarian cancer transcriptome. The package and pipeline for producing it are available from http://bcb.dfci.harvard.edu/ovariancancer. Database URL: http://bcb.dfci.harvard.edu/ovariancance

Aberration in DNA Methylation in B-Cell Lymphomas Has a Complex Origin and Increases with Disease Severity

Despite mounting evidence that epigenetic abnormalities play a key role in cancer biology, their contributions to the malignant phenotype remain poorly understood. Here we studied genome-wide DNA methylation in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and diffuse large B-cell lymphomas. These lymphomas display striking and progressive intra-tumor heterogeneity and also inter-patient heterogeneity in their cytosine methylation patterns. Epigenetic heterogeneity is initiated in normal germinal center B-cells, increases markedly with disease aggressiveness, and is associated with unfavorable clinical outcome. Moreover, patterns of abnormal methylation vary depending upon chromosomal regions, gene density and the status of neighboring genes. DNA methylation abnormalities arise via two distinct processes: i) lymphomagenic transcriptional regulators perturb promoter DNA methylation in a target gene-specific manner, and ii) aberrant epigenetic states tend to spread to neighboring promoters in the absence of CTCF insulator binding sites

An Experimental and Numerical Investigation of Flapping-Wing Propulsion

AIAA Paper No. 99-0995, 37th AIAA Aerospace Sciences Meeting, Reno, Nevada, Jan. 1999.Flapping-wing propulsion is investigated experimentally and numerically with direct comparisons between experimental and numerical thrust measurements for several geometrically simple configurations. Numerical simulations are performed using linear theory, and a previously developed, unsteady panel method that models one or two independently moving airfoils with three-degrees of freedom and non-linear deforming wakes. Experiments are carried out in the Naval Postgraduate School 5'×5' low-speed tunnel. A flapping mechanism that approximates the two-dimensional motions modeled by the panel code is suspended with cables in the wind tunnel, and thrust measurements are made by measuring the streamwise displacement of the model using a laser range-finder. The experimental flapping mechanism utilizes variable aspect-ratio wings and optional tip plates to investigate the effect of three-dimensionality. The device flaps two airfoils, each with two degrees of freedom and adjustable pitch and plunge amplitudes, and additional stationary wings may be attached up and/or downstream of the flapping wings to investigate interference effects

Proton Irradiation of CVD Diamond Detectors for High Luminosity Experiments at the LHC

CVD diamond shows promising properties for use as a position sensitive detector for experiments in the highest radiation areas at the Large Hadron Collider. In order to study the radiation hardn ess of diamond we exposed CVD diamond detector samples to 24~GeV/$c$ and 500~MeV protons up to a fluence of $5\times 10^{15}~p/{\rm cm^2}$. We measured the charge collection distance, the ave rage distance electron hole pairs move apart in an external electric field, and leakage currents before, during, and after irradiation. The charge collection distance remains unchanged up to $1\ times 10^{15}~p/{\rm cm^2}$ and decreases by $\approx$40~\% at $5\times 10^{15}~p/{\rm cm^2}$. Leakage currents of diamond samples were below 1~pA before and after irradiation. The particle indu ced currents during irradiation correlate well with the proton flux. In contrast to diamond, a silicon diode, which was irradiated for comparison, shows the known large increase in leakage curren t. We conclude that CVD diamond detectors are radiation hard to 24~GeV/$c$ and 500~MeV protons up to at least $1\times 10^{15}~p/{\rm cm^2}$ without signal loss

Performance of irradiated CVD diamond micro-strip sensors

CVD diamond detectors are of interest for charged particle detection and tracking due to their high radiation tolerance. In this article we present, for the first time, beam test results from recently manufactured CVD diamond strip detectors and their behavior under low doses of electrons from a $\beta$-source and the performance before and after intense ($>10^{15}/{\rm cm^2}$) proton- and pion-irradiations. We find that low dose irradiations increase the signal-to-noise ratio (pumping of the signal) and slightly deteriorate the spatial resolution. Intense irradiations with protons ($2.2\times 10^{15}~p/{\rm cm^2}$) lowers the signal-to-noise ratio slightly. Intense irradiation with pions ($2.9\times 10^{15}~\pi/{\rm cm^2}$) lowers the signal-to-noise ratio more. The spatial resolution of the diamond sensors improves after irradiations