The 2.3 GHz continuum survey of the GEM project

We present a partial-sky survey of the radio continuum at 2.3 GHz within the scope of the Galactic Emission Mapping (GEM) project, an observational program conceived and developed to reveal the large-scale properties of Galactic synchrotron radiation through a set of self-consistent surveys of the radio continuum between 408 MHz and 10 GHz. The GEM experiment uses a portable and double-shielded 5.5-m radiotelescope in altazimuthal configuration to map 60-degree-wide declination bands from different observational sites by circularly scanning the sky at zenithal angles of 30 deg from a constantly rotating platform. The observations were accomplished with a total power receiver, whose front-end High Electron Mobility Transistor (HEMT) amplifier was matched directly to a cylindrical horn at the prime focus of the parabolic reflector. The Moon was used to calibrate the antenna temperature scale and the preparation of the map required direct subtraction and destriping algorithms to remove ground contamination as the most significant source of systematic error. We used 484 hours of total intensity observations from two locations in Colombia and Brazil to yield 66% sky coverage from DEC = -51.73 deg to DEC = +34.78 deg. The zero-level uncertainty of the combined survey is 103 mK with a temperature scale error of 5% after direct correlation with the Rhodes/HartRAO survey at 2326 MHz on a T-T plot. The sky brightness distribution into regions of low and high emission in the GEM survey is consistent with the appearance of a transition region as seen in the Haslam 408 MHz and WMAP K-band surveys. Preliminary results also show that the temperature spectral index between 408 MHz and the 2.3 GHz band of the GEM survey has a weak spatial correlation with these regions; but it steepens significantly from high to low emission regions with respect to the WMAP K-band survey.Comment: 20 pages, 21 figures, 6 tables. Extensively revised and enlarged version accepted for publication in Astronomy & Astrophysics. Smaller figure

Amplified Loci on Chromosomes 8 and 17 Predict Early Relapse in ER-Positive Breast Cancers

Adjuvant hormonal therapy is administered to all early stage ER+ breast cancers, and has led to significantly improved survival. Unfortunately, a subset of ER+ breast cancers suffer early relapse despite hormonal therapy. To identify molecular markers associated with early relapse in ER+ breast cancer, an outlier analysis method was applied to a published gene expression dataset of 268 ER+ early-stage breast cancers treated with tamoxifen alone. Increased expression of sets of genes that clustered in chromosomal locations consistent with the presence of amplicons at 8q24.3, 8p11.2, 17q12 (HER2 locus) and 17q21.33-q25.1 were each found to be independent markers for early disease recurrence. Distant metastasis free survival (DMFS) after 10 years for cases with any amplicon (DMFS  = 56.1%, 95% CI  = 48.3–63.9%) was significantly lower (P  = 0.0016) than cases without any of the amplicons (DMFS  = 87%, 95% CI  = 76.3% –97.7%). The association between presence of chromosomal amplifications in these regions and poor outcome in ER+ breast cancers was independent of histologic grade and was confirmed in independent clinical datasets. A separate validation using a FISH-based assay to detect the amplicons at 8q24.3, 8p11.2, and 17q21.33-q25.1 in a set of 36 early stage ER+/HER2- breast cancers treated with tamoxifen suggests that the presence of these amplicons are indeed predictive of early recurrence. We conclude that these amplicons may serve as prognostic markers of early relapse in ER+ breast cancer, and may identify novel therapeutic targets for poor prognosis ER+ breast cancers

Array-CGH and breast cancer

The introduction of comparative genomic hybridization (CGH) in 1992 opened new avenues in genomic investigation; in particular, it advanced analysis of solid tumours, including breast cancer, because it obviated the need to culture cells before their chromosomes could be analyzed. The current generation of CGH analysis uses ordered arrays of genomic DNA sequences and is therefore referred to as array-CGH or matrix-CGH. It was introduced in 1998, and further increased the potential of CGH to provide insight into the fundamental processes of chromosomal instability and cancer. This review provides a critical evaluation of the data published on array-CGH and breast cancer, and discusses some of its expected future value and developments

Studying protein–protein affinity and immobilized ligand–protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein–protein and protein–immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS