Comparing computer-generated and pathologist-generated tumour segmentations for immunohistochemical scoring of breast tissue microarrays

BACKGROUND: Tissue microarrays (TMAs) have become a valuable resource for biomarker expression in translational research. Immunohistochemical (IHC) assessment of TMAs is the principal method for analysing large numbers of patient samples, but manual IHC assessment of TMAs remains a challenging and laborious task. With advances in image analysis, computer-generated analyses of TMAs have the potential to lessen the burden of expert pathologist review. METHODS: In current commercial software computerised oestrogen receptor (ER) scoring relies on tumour localisation in the form of hand-drawn annotations. In this study, tumour localisation for ER scoring was evaluated comparing computer-generated segmentation masks with those of two specialist breast pathologists. Automatically and manually obtained segmentation masks were used to obtain IHC scores for thirty-two ER-stained invasive breast cancer TMA samples using FDA-approved IHC scoring software. RESULTS: Although pixel-level comparisons showed lower agreement between automated and manual segmentation masks (κ=0.81) than between pathologists' masks (κ=0.91), this had little impact on computed IHC scores (Allred; [Image: see text]=0.91, Quickscore; [Image: see text]=0.92). CONCLUSIONS: The proposed automated system provides consistent measurements thus ensuring standardisation, and shows promise for increasing IHC analysis of nuclear staining in TMAs from large clinical trials

The Mid-Infrared Instrument for the James Webb Space Telescope, III: MIRIM, The MIRI Imager

In this article, we describe the MIRI Imager module (MIRIM), which provides broad-band imaging in the 5 - 27 microns wavelength range for the James Webb Space Telescope. The imager has a 0"11 pixel scale and a total unobstructed view of 74"x113". The remainder of its nominal 113"x113" field is occupied by the coronagraphs and the low resolution spectrometer. We present the instrument optical and mechanical design. We show that the test data, as measured during the test campaigns undertaken at CEA-Saclay, at the Rutherford Appleton Laboratory, and at the NASA Goddard Space Flight Center, indicate that the instrument complies with its design requirements and goals. We also discuss the operational requirements (multiple dithers and exposures) needed for optimal scientific utilization of the MIRIM.Comment: 29 pages, 9 figure

Immunohistochemical Phenotype of Breast Cancer during 25-Year Follow-up of the Royal Marsden Tamoxifen Prevention Trial.

The randomized, double-blinded Royal Marsden Tamoxifen Breast Cancer Prevention Trial in healthy high-risk women started in 1986 and is still blinded. Eligible participants (n = 2,471) were randomly assigned to tamoxifen (20 mg/d) or placebo for 8 years. Analysis in 2006 showed a 30% risk reduction of estrogen receptor (ER)-positive invasive breast cancer mostly in the posttreatment period. Biomarker analysis in this population may identify any subgroup-specific preventive effects tamoxifen. After a median follow-up of 18.4 years, 242 patients had developed invasive cancer, 134 on placebo and 108 on tamoxifen. From these, 180 tissue blocks were available and ER, progesterone receptor (PgR), Ki67, HER2, and EGFR were immunohistochemically analyzed. A 32% reduction in ER+ and PgR+ invasive cancers resulted after 8 years of treatment. Quantitative levels of ER and PgR were lower in the tamoxifen-treated group, significantly so for ER (P = 0.001). These lower ER levels were restricted to the posttreatment period (P = 0.018). Among the ER+ group, there was a similar proportional decrease in PgR+ and PgR- tumors by tamoxifen. The median levels of Ki67 were similar in both arms. The numbers of HER2-positive and EGFR-positive cancers were higher in the tamoxifen arm but not significantly so. In conclusion, the preventive effects of tamoxifen result in reduced ER-positive but not ER-negative tumors and reduced ER expression in the ER-positive cases largely confined to the posttreatment period. Overall reductions in PgR expression are explained by lower frequency of ER-positive cases. Impact on Ki67, HER2, and EGFR was modest. Cancer Prev Res; 10(3); 171-6. ©2017 AACR

Characterizing Exoplanets in the Visible and Infrared: A Spectrometer Concept for the EChO Space Mission

Transit-spectroscopy of exoplanets is one of the key observational techniques to characterize the extrasolar planet and its atmosphere. The observational challenges of these measurements require dedicated instrumentation and only the space environment allows an undisturbed access to earth-like atmospheric features such as water or carbon-dioxide. Therefore, several exoplanet-specific space missions are currently being studied. One of them is EChO, the Exoplanet Characterization Observatory, which is part of ESA's Cosmic Vision 2015-2025 program, and which is one of four candidates for the M3 launch slot in 2024. In this paper we present the results of our assessment study of the EChO spectrometer, the only science instrument onboard this spacecraft. The instrument is a multi-channel all-reflective dispersive spectrometer, covering the wavelength range from 400 nm to 16 microns simultaneously with a moderately low spectral resolution. We illustrate how the key technical challenge of the EChO mission - the high photometric stability - influences the choice of spectrometer concept and drives fundamentally the instrument design. First performance evaluations underline the fitness of the elaborated design solution for the needs of the EChO mission.Comment: 20 pages, 8 figures, accepted for publication in the Journal of Astronomical Instrumentatio

Variable turbulent convection as the cause of the Blazhko effect - testing the Stothers model

The amplitude and phase modulation observed in a significant fraction of the RR Lyrae variables - the Blazhko effect - represents a long-standing enigma in stellar pulsation theory. No satisfactory explanation for the Blazhko effect has been proposed so far. In this paper we focus on the Stothers (2006) idea, in which modulation is caused by changes in the structure of the outer convective zone, caused by a quasi-periodically changing magnetic field. However, up to this date no quantitative estimates were made to investigate whether such a mechanism can be operational and whether it is capable of reproducing the light variation we observe in Blazhko variables. We address the latter problem. We use a simplified model, in which the variation of turbulent convection is introduced into the non-linear hydrodynamic models in an ad hoc way, neglecting interaction with the magnetic field. We study the light curve variation through the modulation cycle and properties of the resulting frequency spectra. Our results are compared with Kepler observations of RR Lyr. We find that reproducing the light curve variation, as is observed in RR Lyr, requires a huge modulation of the mixing length, of the order of +/-50 per cent, on a relatively short time-scale of less than 40 days. Even then, we are not able to reproduce neither all the observed relations between modulation components present in the frequency spectrum, nor the relations between Fourier parameters describing the shape of the instantaneous light curves.Comment: 17 pages, 13 figures, accepted for publication in MNRAS; for associated animation, see http://homepage.univie.ac.at/radek.smolec/publications/KASC11a

MAGE-A cancer/testis antigens inhibit MDM2 ubiquitylation function and promote increased levels of MDM4

Melanoma antigen A (MAGE-A) proteins comprise a structurally and biochemically similar sub-family of Cancer/Testis antigens that are expressed in many cancer types and are thought to contribute actively to malignancy. MAGE-A proteins are established regulators of certain cancer-associated transcription factors, including p53, and are activators of several RING finger-dependent ubiquitin E3 ligases. Here, we show that MAGE-A2 associates with MDM2, a ubiquitin E3 ligase that mediates ubiquitylation of more than 20 substrates including mainly p53, MDM2 itself, and MDM4, a potent p53 inhibitor and MDM2 partner that is structurally related to MDM2. We find that MAGE-A2 interacts with MDM2 via the N-terminal p53-binding pocket and the RING finger domain of MDM2 that is required for homo/hetero-dimerization and for E2 ligase interaction. Consistent with these data, we show that MAGE-A2 is a potent inhibitor of the E3 ubiquitin ligase activity of MDM2, yet it does not have any significant effect on p53 turnover mediated by MDM2. Strikingly, however, increased MAGE-A2 expression leads to reduced ubiquitylation and increased levels of MDM4. Similarly, silencing of endogenous MAGE-A expression diminishes MDM4 levels in a manner that can be rescued by the proteasomal inhibitor, bortezomid, and permits increased MDM2/MDM4 association. These data suggest that MAGE-A proteins can: (i) uncouple the ubiquitin ligase and degradation functions of MDM2; (ii) act as potent inhibitors of E3 ligase function; and (iii) regulate the turnover of MDM4. We also find an association between the presence of MAGE-A and increased MDM4 levels in primary breast cancer, suggesting that MAGE-A-dependent control of MDM4 levels has relevance to cancer clinically

Functional Magnetic Resonance Imaging in Conscious Animals: A New Tool in Behavioural Neuroscience Research

Functional magnetic resonance imaging (fMRI) is a unique window to the brain, enabling scientists to follow changes in brain activity in response to hormones, ageing, environment, drugs of abuse and other stimuli. In this review, we present a general background to fMRI and the different imaging modalities that can be used in fMRI studies. Included are examples of the application of fMRI in behavioural neuroscience research, along with discussion of the advantages and disadvantages of this technology