ESO Imaging Survey: Infrared Deep Public Survey

This paper presents new J and Ks data obtained from observations conducted at the ESO 3.5m New Technology Telescope using the SOFI camera. These data were taken as part of the ESO Imaging Survey Deep Public Survey (DPS) and significantly extend the earlier optical/infrared EIS-DEEP survey presented in a previous paper. The DPS-IR survey comprises two observing strategies: shallow Ks observations providing nearly full coverage of pointings with complementary multi-band optical data and deeper J and Ks observations of the central parts of these fields. The DPS-IR survey provides a coverage of roughly 2.1 square degrees in Ks with 0.63 square degrees to fainter magnitudes and also covered in J, over three independent regions of the sky. The goal of the present paper is to describe the observations, the data reduction procedures, and to present the final survey products. The astrometric solution with an estimated accuracy of <0.15" is based on the USNO catalog. The final stacked images presented here number 89 and 272, in J and Ks, respectively, the latter reflecting the larger surveyed area. The J and Ks images were taken with a median seeing of 0.77" and 0.8". The images reach a median 5sigma limiting magnitude of J_AB~23.06 in an aperture of 2", while the corresponding limiting magnitude in Ks_AB is ~21.41 and ~22.16 mag for the shallow and deep strategies. Overall, the observed limiting magnitudes are consistent with those originally proposed. The quality of the data has been assessed by comparing the measured magnitude of sources at the bright end directly with those reported by the 2MASS survey and at the faint end by comparing the counts of galaxies and stars with those of other surveys to comparable depth and to model predictions. The final science-grade catalogs and images are available at CDS.Comment: Accepted for publication in A&A, 14 pages, 8 figures, a full resolution version of the paper is available from http://www.astro.ku.dk/~lisbeth/eisdata/papers/5019.pd

First simultaneous optical/near-infrared imaging of an X-ray selected, high-redshift cluster of galaxies with GROND: the galaxy population of XMMU J0338.7+0030 at z=1.1

The XMM-Newton Distant Cluster Project is a serendipitous survey for clusters of galaxies at redshifts z>=0.8 based on deep archival XMM-Newton observations. ... Low-significance candidate high-z clusters are followed up with the seven-channel imager GROND (Gamma-Ray Burst Optical and Near-Infrared Detector) that is mounted at a 2m-class telescope. ... The test case is XMMU J0338.7+0030, suggested to be at z~1.45+/-0.15 from the analysis of the z-H vs H colour-magnitude diagram obtained from the follow-up imaging. Later VLT-FORS2 spectroscopy enabled us to identify four members, which set this cluster at z=1.097+/-0.002. To reach a better knowledge of its galaxy population, we observed XMMU J0338.7+0030 with GROND for about 6 hr. The publicly available photo-z code le Phare was used. The Ks-band number counts of the non-stellar sources out of the 832 detected down to z'~26 AB-mag in the 3.9x4.3 square arcmin region of XMMU J0338.7+0030 imaged at all GROND bands clearly exceed those computed in deep fields/survey areas at ~20.5 - 22.5 AB-mag. The photo-z's of the three imaged spectroscopic members yield z=1.12+/-0.09. The spatial distribution and the properties of the GROND sources with a photo-z in the range 1.01 - 1.23 confirm the correspondence of the X-ray source with a galaxy over-density at a significance of at least 4.3 sigma. Candidate members that are spectro-photometrically classified as elliptical galaxies define a red locus in the i'-z' vs z' colour-magnitude diagram that is consistent with the red sequence of the cluster RDCS J0910+5422 at z=1.106. XMMU J0338.7+0030 hosts also a population of bluer late-type spirals and irregulars. The starbursts among the photometric members populate both loci, consistently with previous results. The analysis of the available data set indicates that XMMU J0338.7+0030 is a low-mass cluster (M_200 ~ 1E14 M_sun) at z=1.1. (Abridged)Comment: accepted for publication in Astronomy & Astrophysics Main Journal, 27 pages, 24 figures, 1 tabl

Soil Moisture and Fungi Affect Seed Survival in California Grassland Annual Plants

Survival of seeds in the seed bank is important for the population dynamics of many plant species, yet the environmental factors that control seed survival at a landscape level remain poorly understood. These factors may include soil moisture, vegetation cover, soil type, and soil pathogens. Because many soil fungi respond to moisture and host species, fungi may mediate environmental drivers of seed survival. Here, I measure patterns of seed survival in California annual grassland plants across 15 species in three experiments. First, I surveyed seed survival for eight species at 18 grasslands and coastal sage scrub sites ranging across coastal and inland Santa Barbara County, California. Species differed in seed survival, and soil moisture and geographic location had the strongest influence on survival. Grasslands had higher survival than coastal sage scrub sites for some species. Second, I used a fungicide addition and exotic grass thatch removal experiment in the field to tease apart the relative impact of fungi, thatch, and their interaction in an invaded grassland. Seed survival was lower in the winter (wet season) than in the summer (dry season), but fungicide improved winter survival. Seed survival varied between species but did not depend on thatch. Third, I manipulated water and fungicide in the laboratory to directly examine the relationship between water, fungi, and survival. Seed survival declined from dry to single watered to continuously watered treatments. Fungicide slightly improved seed survival when seeds were watered once but not continually. Together, these experiments demonstrate an important role of soil moisture, potentially mediated by fungal pathogens, in driving seed survival

Effect of neoadjuvant treatment with anastrozole on tumour histology in postmenopausal women with large operable breast cancer

Anastrozole is an orally active, non-steroidal aromatase inhibitor which appears effective as neoadjuvant treatment of breast cancer. Histological changes have been evaluated in biopsies from large, oestrogen-receptor rich, operable breast tumours in postmenopausal women following 12 weeks of neoadjuvant anastrozole treatment (1 mg (n=12) or 10 mg (n=11)). Of the 23 patients, 18 had a clinical response following treatment. Compared with pre-treatment biopsies anastrozole-treated specimens displayed decreased cellularity and/or increased fibrosis in 15 tumours; changes in gland formation, nuclear pleomorphism, or mitoses, in 12 cases; and a reduction in Mib1 score in all tumours. Marked changes in apoptotic scores were seen following treatment but the direction of effect was inconsistent. In all 17 tumours which were positive for progesterone receptors before therapy, treatment was associated with reduced staining for progesterone receptors. There was no consistent effect of treatment on oestrogen-receptor expression. It is concluded that neoadjuvant anastrozole treatment in this patient group has marked effects on tumour histopathology but these do not always correlate with clinical response

What Was I Thinking? Eye-Tracking Experiments Underscore the Bias that Architecture Exerts on Nuclear Grading in Prostate Cancer

We previously reported that nuclear grade assignment of prostate carcinomas is subject to a cognitive bias induced by the tumor architecture. Here, we asked whether this bias is mediated by the non-conscious selection of nuclei that “match the expectation” induced by the inadvertent glance at the tumor architecture. 20 pathologists were asked to grade nuclei in high power fields of 20 prostate carcinomas displayed on a computer screen. Unknown to the pathologists, each carcinoma was shown twice, once before a background of a low grade, tubule-rich carcinoma and once before the background of a high grade, solid carcinoma. Eye tracking allowed to identify which nuclei the pathologists fixated during the 8 second projection period. For all 20 pathologists, nuclear grade assignment was significantly biased by tumor architecture. Pathologists tended to fixate on bigger, darker, and more irregular nuclei when those were projected before kigh grade, solid carcinomas than before low grade, tubule-rich carcinomas (and vice versa). However, the morphometric differences of the selected nuclei accounted for only 11% of the architecture-induced bias, suggesting that it can only to a small part be explained by the unconscious fixation on nuclei that “match the expectation”. In conclusion, selection of « matching nuclei » represents an unconscious effort to vindicate the gravitation of nuclear grades towards the tumor architecture

Reconstructing CNV genotypes using segregation analysis: combining pedigree information with CNV assay

<p>Abstract</p> <p>Background</p> <p>Repeated blocks of genome sequence have been shown to be associated with genetic diversity and disease risk in humans, and with phenotypic diversity in model organisms and domestic animals. Reliable tests are desirable to determine whether individuals are carriers of copy number variants associated with disease risk in humans and livestock, or associated with economically important traits in livestock. In some cases, copy number variants affect the phenotype through a dosage effect but in other cases, allele combinations have non-additive effects. In the latter cases, it has been difficult to develop tests because assays typically return an estimate of the sum of the copy number counts on the maternally and paternally inherited chromosome segments, and this sum does not uniquely determine the allele configuration. In this study, we show that there is an old solution to this new problem: segregation analysis, which has been used for many years to infer alleles in pedigreed populations.</p> <p>Methods</p> <p>Segregation analysis was used to estimate copy number alleles from assay data on simulated half-sib sheep populations. Copy number variation at the Agouti locus, known to be responsible for the recessive self-colour black phenotype, was used as a model for the simulation and an appropriate penetrance function was derived. The precision with which carriers and non-carriers of the undesirable single copy allele could be identified, was used to evaluate the method for various family sizes, assay strategies and assay accuracies.</p> <p>Results</p> <p>Using relationship data and segregation analysis, the probabilities of carrying the copy number alleles responsible for black or white fleece were estimated with much greater precision than by analyzing assay results for animals individually. The proportion of lambs correctly identified as non-carriers of the undesirable allele increased from 7% when the lambs were analysed alone to 80% when the lambs were analysed in half-sib families.</p> <p>Conclusions</p> <p>When a quantitative assay is used to estimate copy number alleles, segregation analysis of related individuals can greatly improve the precision of the estimates. Existing software for segregation analysis would require little if any change to accommodate the penetrance function for copy number assay data.</p