Chemical evolution in the early phases of massive star formation II: Deuteration

The chemical evolution in high-mass star-forming regions is still poorly constrained. Studying the evolution of deuterated molecules allows to differentiate between subsequent stages of high-mass star formation regions due to the strong temperature dependence of deuterium isotopic fractionation. We observed a sample of 59 sources including 19 infrared dark clouds, 20 high-mass protostellar objects, 11 hot molecular cores and 9 ultra-compact HII regions in the (3-2) transitions of the four deuterated molecules, DCN, DNC, DCO+ and N2D+ as well as their non-deuterated counterpart. The overall detection fraction of DCN, DNC and DCO+ is high and exceeds 50% for most of the stages. N2D+ was only detected in a few infrared dark clouds and high-mass protostellar objects. It can be related to problems in the bandpass at the frequency of the transition and to low abundances in the more evolved, warmer stages. We find median D/H ratios of ~0.02 for DCN, ~0.005 for DNC, ~0.0025 for DCO+ and ~0.02 for N2D+. While the D/H ratios of DNC, DCO+ and N2D+ decrease with time, DCN/HCN peaks at the hot molecular core stage. We only found weak correlations of the D/H ratios for N2D+ with the luminosity of the central source and the FWHM of the line, and no correlation with the H2 column density. In combination with a previously observed set of 14 other molecules (Paper I) we fitted the calculated column densities with an elaborate 1D physico-chemical model with time-dependent D-chemistry including ortho- and para-H2 states. Good overall fits to the observed data have been obtained the model. It is one of the first times that observations and modeling have been combined to derive chemically based best-fit models for the evolution of high-mass star formation including deuteration.Comment: 26 pages, 16 figures, accepted at A&

Chemical evolution in the early phases of massive star formation. I

Understanding the chemical evolution of young (high-mass) star-forming regions is a central topic in star formation research. Chemistry is employed as a unique tool 1) to investigate the underlying physical processes and 2) to characterize the evolution of the chemical composition. We observed a sample of 59 high-mass star-forming regions at different evolutionary stages varying from the early starless phase of infrared dark clouds to high-mass protostellar objects to hot molecular cores and, finally, ultra-compact HII regions at 1mm and 3mm with the IRAM 30m telescope. We determined their large-scale chemical abundances and found that the chemical composition evolves along with the evolutionary stages. On average, the molecular abundances increase with time. We modeled the chemical evolution, using a 1D physical model where density and temperature vary from stage to stage coupled with an advanced gas-grain chemical model and derived the best-fit chi^2 values of all relevant parameters. A satisfying overall agreement between observed and modeled column densities for most of the molecules was obtained. With the best-fit model we also derived a chemical age for each stage, which gives the timescales for the transformation between two consecutive stages. The best-fit chemical ages are ~10,000 years for the IRDC stage, ~60,000 years for the HMPO stage, ~40,000 years for the HMC stage, and ~10,000 years for the UCHII stage. The total chemical timescale for the entire evolutionary sequence of the high-mass star formation process is on the order of 10^5 years, which is consistent with theoretical estimates. Furthermore, based on the approach of a multiple-line survey of unresolved data, we were able to constrain an intuitive and reasonable physical and chemical model. The results of this study can be used as chemical templates for the different evolutionary stages in high-mass star formation.Comment: 31 pages, 11 figures, 21 tables, accepted by A&A; typos adde

High-precision photometry by telescope defocusing - V.WASP-15 and WASP-16

We present newphotometric observations ofWASP-15 andWASP-16, two transiting extrasolar planetary systems with measured orbital obliquities but without photometric follow-up since their discovery papers. Our new data for WASP-15 comprise observations of one transit simultaneously in four optical passbands using GROND on the MPG/European Southern Observatory (ESO) 2.2 m telescope, plus coverage of half a transit from DFOSC on the Danish 1.54 m telescope, both at ESO La Silla. ForWASP-16 we present observations of fourcomplete transits, all from the Danish telescope. We use these new data to refine the measured physical properties and orbital ephemerides of the two systems. Whilst our results are close to the originally determined values forWASP-15, we find that the star and planet in theWASP-16 system are both larger and less massive than previously thought. ©2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society

Physical properties, transmission and emission spectra of the WASP-19 planetary system from multi-colour photometry

We present new ground-based, multi-colour, broad-band photometric measurements of the physical parameters, transmission and emission spectra of the transiting extrasolar planet WASP-19b. The measurements are based on observations of eight transits and four occultations through a Gunn i filter using the 1.54-m Danish Telescope, 14 transits through an Rc filter at the Perth Exoplanet SurveyTelescope (PEST) observatory and one transit observed simultaneously through four optical (Sloan g\u27, r\u27, i\u27, z\u27) and three near-infrared (J,H,K) filters, using the Gamma Ray Burst Optical and Near-Infrared Detector (GROND) instrument on the MPG/ESO 2.2-m telescope. The GROND optical light curves have a point-to-point scatter around the best-fitting model between 0.52 and 0.65 mmag rms. We use these new data to measure refined physical parameters for the system. We find the planet to be more bloated (Rb = 1.410 ± 0.017RJup; Mb = 1.139 ± 0.030MJup) and the system to be twice as old as initially thought. We also used published and archived data sets to study the transit timings, which do not depart from a linear ephemeris. We detected an anomaly in the GROND transit light curve which is compatible with a spot on the photosphere of the parent star. The starspot position, size, spot contrast and temperature were established. Using our new and published measurements, we assembled the planet\u27s transmission spectrum over the 370-2350 nm wavelength range and its emission spectrum over the 750-8000 nm range. By comparing these data to theoretical models we investigated the theoretically predicted variation of the apparent radius of WASP- 19b as a function of wavelength and studied the composition and thermal structure of its atmosphere. We conclude that: (i) there is no evidence for strong optical absorbers at low pressure, supporting the common idea that the planet\u27s atmosphere lacks a dayside inversion; (ii) the temperature of the planet is not homogenized, because the high warming of its dayside causes the planet to be more efficient in re-radiating than redistributing energy to the night side; (iii) the planet seems to be outside of any current classification scheme. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society

The gene normalization task in BioCreative III

BACKGROUND: We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 fully and 500 partially annotated articles were prepared. A total of 507 articles were selected as the test set. Due to the high annotation cost, it was not feasible to obtain gold-standard human annotations for all test articles. Instead, we developed an Expectation Maximization (EM) algorithm approach for choosing a small number of test articles for manual annotation that were most capable of differentiating team performance. Moreover, the same algorithm was subsequently used for inferring ground truth based solely on team submissions. We report team performance on both gold standard and inferred ground truth using a newly proposed metric called Threshold Average Precision (TAP-k). RESULTS: We received a total of 37 runs from 14 different teams for the task. When evaluated using the gold-standard annotations of the 50 articles, the highest TAP-k scores were 0.3297 (k=5), 0.3538 (k=10), and 0.3535 (k=20), respectively. Higher TAP-k scores of 0.4916 (k=5, 10, 20) were observed when evaluated using the inferred ground truth over the full test set. When combining team results using machine learning, the best composite system achieved TAP-k scores of 0.3707 (k=5), 0.4311 (k=10), and 0.4477 (k=20) on the gold standard, representing improvements of 12.4%, 21.8%, and 26.6% over the best team results, respectively. CONCLUSIONS: By using full text and being species non-specific, the GN task in BioCreative III has moved closer to a real literature curation task than similar tasks in the past and presents additional challenges for the text mining community, as revealed in the overall team results. By evaluating teams using the gold standard, we show that the EM algorithm allows team submissions to be differentiated while keeping the manual annotation effort feasible. Using the inferred ground truth we show measures of comparative performance between teams. Finally, by comparing team rankings on gold standard vs. inferred ground truth, we further demonstrate that the inferred ground truth is as effective as the gold standard for detecting good team performance

Cancer chemoprevention: lessons learned and future directions

The concept of delaying or preventing epithelial transformation remains a viable and attainable goal for the future. Drug-based strategies for chemoprevention of the future may predominantly rely upon targeted therapies with tolerable but defined toxicities for treatment of individuals diagnosed with intraepithelial neoplasias. Foods, diet manipulation strategies, or nutraceuticals may be more appropriate to delay or prevent carcinogenesis progression in healthy populations with genetic or epidemiologic evidence of risk for future transformation

Lipid bodies containing oxidatively truncated lipids block antigen cross-presentation by dendritic cells in cancer

Tumor-associated dendritic cells are defective in their ability to cross-present antigens, and they accumulate lipid bodies. Here the authors show that this defect is due to an impaired trafficking of peptide-MHC class I caused by the interaction of electrophilic lipids with chaperone heat shock protein 70