Construction of two whole genome radiation hybrid panels for dromedary (Camelus dromedarius): 5000RAD and 15000RAD

The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools

Structure and oxidation kinetics of the Si(100)-SiO2 interface

We present first-principles calculations of the structural and electronic properties of Si(001)-SiO2 interfaces. We first arrive at reasonable structures for the c-Si/a-SiO2 interface via a Monte-Carlo simulated annealing applied to an empirical interatomic potential, and then relax these structures using first-principles calculations within the framework of density-functional theory. We find a transition region at the interface, having a thickness on the order of 20\AA, in which there is some oxygen deficiency and a corresponding presence of sub-oxide Si species (mostly Si^+2 and Si^+3). Distributions of bond lengths and bond angles, and the nature of the electronic states at the interface, are investigated and discussed. The behavior of atomic oxygen in a-SiO2 is also investigated. The peroxyl linkage configuration is found to be lower in energy than interstitial or threefold configurations. Based on these results, we suggest a possible mechanism for oxygen diffusion in a-SiO2 that may be relevant to the oxidation process.Comment: 7 pages, two-column style with 6 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#ng_sio

Gaia eclipsing binary and multiple systems. Two-Gaussian models applied to OGLE-III eclipsing binary light curves in the Large Magellanic Cloud

The advent of large scale multi-epoch surveys raises the need for automated light curve (LC) processing. This is particularly true for eclipsing binaries (EBs), which form one of the most populated types of variable objects. The Gaia mission, launched at the end of 2013, is expected to detect of the order of few million EBs over a 5-year mission. We present an automated procedure to characterize EBs based on the geometric morphology of their LCs with two aims: first to study an ensemble of EBs on a statistical ground without the need to model the binary system, and second to enable the automated identification of EBs that display atypical LCs. We model the folded LC geometry of EBs using up to two Gaussian functions for the eclipses and a cosine function for any ellipsoidal-like variability that may be present between the eclipses. The procedure is applied to the OGLE-III data set of EBs in the Large Magellanic Cloud (LMC) as a proof of concept. The bayesian information criterion is used to select the best model among models containing various combinations of those components, as well as to estimate the significance of the components. Based on the two-Gaussian models, EBs with atypical LC geometries are successfully identified in two diagrams, using the Abbe values of the original and residual folded LCs, and the reduced $\chi^2$. Cleaning the data set from the atypical cases and further filtering out LCs that contain non-significant eclipse candidates, the ensemble of EBs can be studied on a statistical ground using the two-Gaussian model parameters. For illustration purposes, we present the distribution of projected eccentricities as a function of orbital period for the OGLE-III set of EBs in the LMC, as well as the distribution of their primary versus secondary eclipse widths.Comment: 20 pages, 29 figures. Submitted to A&

Structure and energetics of the Si-SiO_2 interface

Silicon has long been synonymous with semiconductor technology. This unique role is due largely to the remarkable properties of the Si-SiO_2 interface, especially the (001)-oriented interface used in most devices. Although Si is crystalline and the oxide is amorphous, the interface is essentially perfect, with an extremely low density of dangling bonds or other electrically active defects. With the continual decrease of device size, the nanoscale structure of the silicon/oxide interface becomes more and more important. Yet despite its essential role, the atomic structure of this interface is still unclear. Using a novel Monte Carlo approach, we identify low-energy structures for the interface. The optimal structure found consists of Si-O-Si "bridges" ordered in a stripe pattern, with very low energy. This structure explains several puzzling experimental observations.Comment: LaTex file with 4 figures in GIF forma

Systematic and random errors between collocated satellite ice water path observations

There remains large disagreement between ice-water path (IWP) in observational data sets, largely because the sensors observe different parts of the ice particle size distribution. A detailed comparison of retrieved IWP from satellite observations in the Tropics (!30 " latitude) in 2007 was made using collocated measurements. The radio detection and ranging(radar)/light detection and ranging (lidar) (DARDAR) IWP data set, based on combined radar/lidar measurements, is used as a reference because it provides arguably the best estimate of the total column IWP. For each data set, usable IWP dynamic ranges are inferred from this comparison. IWP retrievals based on solar reflectance measurements, in the moderate resolution imaging spectroradiometer (MODIS), advanced very high resolution radiometer–based Climate Monitoring Satellite Applications Facility (CMSAF), and Pathfinder Atmospheres-Extended (PATMOS-x) datasets, were found to be correlated with DARDAR over a large IWP range (~20–7000 g m -2 ). The random errors of the collocated data sets have a close to lognormal distribution, and the combined random error of MODIS and DARDAR is less than a factor of 2, which also sets the upper limit for MODIS alone. In the same way, the upper limit for the random error of all considered data sets is determined. Data sets based on passive microwave measurements, microwave surface and precipitation products system (MSPPS), microwave integrated retrieval system (MiRS), and collocated microwave only (CMO), are largely correlated with DARDAR for IWP values larger than approximately 700 g m -2 . The combined uncertainty between these data sets and DARDAR in this range is slightly less MODIS-DARDAR, but the systematic bias is nearly an order of magnitude

In utero exposure to cigarette smoke dysregulates human fetal ovarian developmental signalling

STUDY QUESTION How does maternal cigarette smoking disturb development of the human fetal ovary?<p></p> SUMMARY ANSWER Maternal smoking increases fetal estrogen titres and dysregulates several developmental processes in the fetal ovary.<p></p> WHAT IS KNOWN ALREADY Exposure to maternal cigarette smoking during gestation reduces human fetal ovarian cell numbers, germ cell proliferation and subsequent adult fecundity.<p></p> STUDY DESIGN, SIZE, DURATION The effects of maternal cigarette smoking on the second trimester human fetal ovary, fetal endocrine signalling and fetal chemical burden were studied. A total of 105 fetuses were studied, 56 from mothers who smoked during pregnancy and 49 from those who did not.<p></p> PARTICIPANTS/MATERIALS, SETTING METHODS Ovary, liver and plasma samples were collected from electively terminated, normally progressing, second trimester human fetuses. Circulating fetal hormones, levels of 73 fetal ovarian transcripts, protein localization, density of oocytes/primordial follicles and levels of 16 polycyclic aromatic hydrocarbons (PAHs) in the fetal liver were determined.<p></p> MAIN RESULTS AND THE ROLE OF CHANCE Circulating fetal estrogen levels were very high and were increased by maternal smoking (ANOVA, P = 0.055–0.004 versus control). Smoke exposure also dysregulated (two-way ANOVA, smoking versus gestation weeks interaction, P = 0.046–0.023) four fetal ovarian genes (cytochrome P450 scc [CYP11A1], NOBOX oogenesis homeobox [NOBOX], activator of apoptosis harakiri [HRK], nuclear receptor subfamily 2, group E, member 1 [NR2E1]), shifted the ovarian Inhibin βA/inhibin α ratio (NHBA/INHA) transcript ratio in favour of activin (ANOVA, P = 0.049 versus control) and reduced the proportion of dominant-negative estrogen receptor 2 (ERβ: ESR2) isoforms in half the exposed fetuses. PAHs, ligands for the aryl hydrocarbon receptor (AHR), were increased nearly 6-fold by maternal smoking (ANOVA, P = 0.011 versus control). A fifth transcript, COUP transcription factor 1 (nuclear receptor subfamily 2, group F, member 1: NR2F1, which contains multiple AHR-binding sites), was both significantly increased (ANOVA, P = 0.026 versus control) and dysregulated by (two-way ANOVA, smoking versus gestation weeks interaction, P = 0.021) maternal smoking. NR2F1 is associated with repression of FSHR expression and smoke-exposed ovaries failed to show the normal increase in FSHR expression during the second trimester. There was a significantly higher number of DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 (DDX4) VASA-positive (ANOVA, P = 0.016 versus control), but not POU domain, class 1, transcription factor 1 (POU5F1) OCT3/4-positive, oocytes in smoke-exposed fetuses and this matched with a significantly higher number of primordial follicles (ANOVA, P = 0.024 versus control).<p></p> LIMITATIONS, REASONS FOR CAUTION The effects of maternal smoking on establishment of the maximum fetal primordial follicle pool cannot be reliably studied in our population since the process is not completed until 28 weeks of gestation and normal fetuses older than 21 weeks of gestation are not available for study. Our data suggest that some fetal ovaries are affected by smoke exposure while others are not, indicating that additional studies, with larger numbers, may show more significant effects.<p></p> WIDER IMPLICATIONS OF THE FINDINGS Fetal exposure to chemicals in cigarette smoke is known to lead to reduced fecundity in women. Our study suggests, for the first time, that this occurs via mechanisms involving activation of AHR, disruption of inhibin/activin and estrogen signalling, increased exposure to estrogen and dysregulation of multiple molecular pathways in the exposed human fetal ovary. Our data also suggest that alterations in the ESR2 positive and dominant negative isoforms may be associated with reduced sensitivity of some fetuses to increased estrogens and maternal smoking

Determination of rotation periods in solar-like stars with irregular sampling: the Gaia case

We present a study on the determination of rotation periods (P) of solar-like stars from the photometric irregular time-sampling of the ESA Gaia mission, currently scheduled for launch in 2013, taking into account its dependence on ecliptic coordinates. We examine the case of solar-twins as well as thousands of synthetic time-series of solar-like stars rotating faster than the Sun. In the case of solar twins we assume that the Gaia unfiltered photometric passband G will mimic the variability of the total solar irradiance (TSI) as measured by the VIRGO experiment. For stars rotating faster than the Sun, light-curves are simulated using synthetic spectra for the quiet atmosphere, the spots, and the faculae combined by applying semi-empirical relationships relating the level of photospheric magnetic activity to the stellar rotation and the Gaia instrumental response. The capabilities of the Deeming, Lomb-Scargle, and Phase Dispersion Minimisation methods in recovering the correct rotation periods are tested and compared. The false alarm probability (FAP) is computed using Monte Carlo simulations and compared with analytical formulae. The Gaia scanning law makes the rate of correct detection of rotation periods strongly dependent on the ecliptic latitude (beta). We find that for P ~ 1 d, the rate of correct detection increases with ecliptic latitude from 20-30 per cent at beta ~ 0{\deg} to a peak of 70 per cent at beta=45{\deg}, then it abruptly falls below 10 per cent at beta > 45{\deg}. For P > 5 d, the rate of correct detection is quite low and for solar twins is only 5 per cent on average.Comment: 12 pages, 18 figures, accepted by MNRA

Gaia Data Release 3. The first Gaia catalogue of eclipsing binary candidates

We present the first Gaia catalogue of eclipsing binary candidates released in Gaia DR3, describe its content, provide tips for its usage, estimate its quality, and show illustrative samples. The catalogue contains 2,184,477 sources with G magnitudes up to 20 mag. Candidate selection is based on the results of variable object classification performed within the Gaia Data Processing and Analysis Consortium, further filtered using eclipsing binary-tailored criteria based on the G light curves. To find the orbital period, a large ensemble of trial periods is first acquired using three distinct period search methods applied to the cleaned G light curve. The G light curve is then modelled with up-to two Gaussians and a cosine for each trial period. The best combination of orbital period and geometric model is finally selected using Bayesian model comparison based on the BIC. A global ranking metric is provided to rank the quality of the chosen model between sources. The catalogue is restricted to orbital periods larger than 0.2 days. About 530,000 of the candidates are classified as eclipsing binaries in the literature as well, out of ~600,000 available crossmatches, and 93% of them have published periods compatible with the Gaia periods. Catalogue completeness is estimated to be between 25% and 50%, depending on the sky region, relative to the OGLE4 catalogues of eclipsing binaries towards the Galactic Bulge and the Magellanic Clouds. The analysis of an illustrative sample of ~400,000 candidates with significant parallaxes shows properties in the observational HR diagram as expected for eclipsing binaries. The subsequent analysis of a sub-sample of detached bright candidates provides further hints for the exploitation of the catalogue. The orbital periods, light curve model parameters, and global rankings are all published in the catalogue with their related uncertainties where applicable.Comment: Submitted to A&A. Main text: 23 pages, 35 figures. Four appendices (17 pages) with 38 figure

A multi-instrument comparison of integrated water vapour measurements at a high latitude site

We compare measurements of integrated water vapour (IWV) over a subarctic site (Kiruna, Northern Sweden) from five different sensors and retrieval methods: Radiosondes, Global Positioning System (GPS), ground-based Fourier-transform infrared (FTIR) spectrometer, groundbased microwave radiometer, and satellite-based microwave radiometer (AMSU-B). Additionally, we compare also to ERA-Interim model reanalysis data. GPS-based IWV data have the highest temporal coverage and resolution and are chosen as reference data set. All datasets agree reasonably well, but the ground-based microwave instrument only if the data are cloud-filtered. We also address two issues that are general for such intercomparison studies, the impact of different lower altitude limits for the IWV integration, and the impact of representativeness error. We develop methods for correcting for the former, and estimating the random error contribution of the latter. A literature survey reveals that reported systematic differences between different techniques are study-dependent and show no overall consistent pattern. Further improving the absolute accuracy of IWV measurements and providing climate-quality time series therefore remain challenging problems

Recent results from Pb-Au collisions at 158 GeV/c per nucleon obtained with the CERES spectrometer

During the 1996 lead run time, CERES has accumulated 42 million events, corresponding to a factor of 5 more statistics than in 1995 and 2.5 million events of a special photon-run. We report on the results of the low-mass e$^+$e$^-$-pair analysis. Since the most critical item is the poor signal-to-background ratio we also discuss the understanding of this background, in absolute terms, with the help of a detailed Monte Carlo simulation. We show preliminary results of the photon analysis and summarize the results of the hadron analysis preliminarily reported on already at QM'97Comment: 10 pages, 9 figures, Proceedings of the XIV Int. Conf. on Nucleus-Nucleus Collisions,Quark Matter 99, Torino, Italy, May 10 - 15, 199