138 research outputs found
Fundamental parameters of Be stars located in the seismology fields of COROT
In preparation for the COROT space mission, we determined the fundamental
parameters (spectral type, temperature, gravity, vsini) of the Be stars
observable by COROT in its seismology fields (64 Be stars). We applied a
careful and detailed modeling of the stellar spectra, taking into account the
veiling caused by the envelope, as well as the gravitational darkening and
stellar flattening due to rapid rotation. Evolutionary tracks for fast rotators
were used to derive stellar masses and ages. The derived parameters will be
used to select Be stars as secondary targets (i.e. observed for 5 consecutive
months) and short-run targets of the COROT mission. Furthermore, we note that
the main part of our stellar sample is falling in the second half of the main
sequence life time, and that in most cases the luminosity class of Be stars is
inaccurate in characterizing their evolutionary status.Comment: 25 pages, 9 figures, Accepted for publication in A&
Bayesian hierarchical clustering for studying cancer gene expression data with unknown statistics
Clustering analysis is an important tool in studying gene expression data. The Bayesian hierarchical clustering (BHC) algorithm can automatically infer the number of clusters and uses Bayesian model selection to improve clustering quality. In this paper, we present an extension of the BHC algorithm. Our Gaussian BHC (GBHC) algorithm represents data as a mixture of Gaussian distributions. It uses normal-gamma distribution as a conjugate prior on the mean and precision of each of the Gaussian components. We tested GBHC over 11 cancer and 3 synthetic datasets. The results on cancer datasets show that in sample clustering, GBHC on average produces a clustering partition that is more concordant with the ground truth than those obtained from other commonly used algorithms. Furthermore, GBHC frequently infers the number of clusters that is often close to the ground truth. In gene clustering, GBHC also produces a clustering partition that is more biologically plausible than several other state-of-the-art methods. This suggests GBHC as an alternative tool for studying gene expression data. The implementation of GBHC is available at https://sites.
google.com/site/gaussianbhc
Effects of gravitational darkening on the determination of fundamental parameters in fast rotating B-type stars
In this paper we develop a calculation code to account for the effects
carried by fast rotation on the observed spectra of early-type stars. Stars are
assumed to be in rigid rotation and the grid of plane-parallel model
atmospheres used to represent the gravitational darkening are calculated by
means of a non-LTE approach. Attention is paid on the relation between the
apparent and parent non-rotating counterpart stellar fundamental parameters and
apparent and true vsini parameters as a function of the rotation rate
Omega/Omega_c, stellar mass and inclination angle. It is shown that omission of
gravitational darkening in the analysis of chemical abundances of CNO elements
can produce systematic overestimation or underestimation, depending on the
lines used, rotational rate and inclination angle. The proximity of Be stars to
the critical rotation is re-discussed by correcting not only the vsini of 130
Be stars, but also their effective temperature and gravity to account for
stellar rotationally induced geometrical distortion and for the concomitant
gravitational darkening effect. We concluded that the increase of the vsini
estimate is accompanied by an even higher value of the stellar equatorial
critical velocity, so that the most probable average rate of angular velocity
of Be stars attains Omega/Omega_c ~ 0.88.Comment: 20 pages, 16 figures. Submitted for publication in A&
How exactly did the Universe become neutral?
We present a refined treatment of H, He I, and He II recombination in the
early Universe. The difference from previous calculations is that we use
multi-level atoms and evolve the population of each level with redshift by
including all bound-bound and bound-free transitions. In this framework we
follow several hundred atomic energy levels for H, He I, and He II combined.
The main improvements of this method over previous recombination calculations
are: (1) allowing excited atomic level populations to depart from an
equilibrium distribution; (2) replacing the total recombination coefficient
with recombination to and photoionization from each level directly at each
redshift step; and (3) correct treatment of the He I atom, including the
triplet and singlet states. We find that the ionization fraction x_e = n_e/n_H
is approximately 10% smaller at redshifts <~800 than in previous calculations,
due to the non-equilibrium of the excited states of H, which is caused by the
strong but cool radiation field at those redshifts. In addition we find that He
I recombination is delayed compared with previous calculations, and occurs only
just before H recombination. These changes in turn can affect the predicted
power spectrum of microwave anisotropies at the few percent level. Other
improvements such as including molecular and ionic species of H, including
complete heating and cooling terms for the evolution of the matter temperature,
including collisional rates, and including feedback of the secondary spectral
distortions on the radiation field, produce negligible change to x_e. The lower
x_e at low z found in this work affects the abundances of H molecular and ionic
species by 10-25%. However this difference is probably not larger than other
uncertainties in the reaction rates.Comment: 24 pages, including 18 figures, using emulateapj.sty, to appear in
ApJ, the code recfast can be obtained at
http://www.astro.ubc.ca/people/scott/recfast.html (in FORTRAN) and
http://cfa-www.harvard.edu/~sasselov/rec/ (in C
Fibrodysplasia Ossificans Progressiva: what have we achieved and where are we now? follow-up to the 2015 Lorentz Workshop
Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare progressive genetic disease effecting one in a million individuals. During their life, patients with FOP progressively develop bone in the soft tissues resulting in increasing immobility and early death. A mutation in the ACVR1 gene was identified as the causative mutation of FOP in 2006. After this, the pathophysiology of FOP has been further elucidated through the efforts of research groups worldwide. In 2015, a workshop was held to gather these groups and discuss the new challenges in FOP research. Here we present an overview and update on these topics
Chemical composition of Galactic OB stars I. CNO abundances in O9 stars
We present NLTE abundances of CNO for a sample of four O9 stars in the
Galaxy, together with new determinations of their stellar parameters, , , (He) and microturbulence. These new analyses take
into account the effect of {\it line--blocking} in the spectral synthesis with
our classical NLTE, plane--parallel and hydrostatic model atmospheres. The
sample includes three O9 He normal stars: two dwarfs, HD 214680 and HD 34078,
and one supergiant, HD 209975, and one fast rotating giant with a preliminary
high He overabundance, HD 191423 with (He)=0.20. We find first that
the consideration of microturbulence in the spectral synthesis for the fast
rotator leads to a considerably lower He abundance, (He)=0.12. The
CNO abundances of the three He normal stars are in good agreement with the
values in the literature for Galactic B dwarfs with no evidence of mixing, and
show that they all have the same chemical composition. We also discuss however
the possible CNO contamination of the supergiant HD 209975. For the fast
rotator we find that the abundances show the trend of the CNO contamination: a
N overabundance together with C and O depletion. The N/C and N/O ratios of our
stars as a function of their projected rotational velocities are consistent
with the predictions of the recent evolutionary models of Meynet & Maeder
[Mey&Mae00].Comment: 19 pages, 12 figures, 13 tables, accepted by A&
NERO - A Post Maximum Supernova Radiation Transport Code
The interpretation of supernova (SN) spectra is essential for deriving SN
ejecta properties such as density and composition, which in turn can tell us
about their progenitors and the explosion mechanism. A very large number of
atomic processes are important for spectrum formation. Several tools for
calculating SN spectra exist, but they mainly focus on the very early or late
epochs. The intermediate phase, which requires a NLTE treatment of radiation
transport has rarely been studied. In this paper we present a new SN radiation
transport code, NERO, which can look at those epochs. All the atomic processes
are treated in full NLTE, under a steady-state assumption. This is a valid
approach between roughly 50 and 500 days after the explosion depending on SN
type. This covers the post-maximum photospheric and the early and the
intermediate nebular phase. As a test, we compare NERO to the radiation
transport code of Jerkstrand et al. (2011) and to the nebular code of Mazzali
et al. (2001). All three codes have been developed independently and a
comparison provides a valuable opportunity to investigate their reliability.
Currently, NERO is one-dimensional and can be used for predicting spectra of
synthetic explosion models or for deriving SN properties by spectral modelling.
To demonstrate this, we study the spectra of the 'normal' SN Ia 2005cf between
50 and 350 days after the explosion and identify most of the common SN Ia line
features at post maximum epochs.Comment: 9 pages, 14 figures, submitted to MNRA
Effect of roflumilast on inflammatory cells in the lungs of cigarette smoke-exposed mice
<p>Abstract</p> <p>Background</p> <p>We reported that roflumilast, a phosphodiesterase 4 inhibitor, given orally at 5 mg/kg to mice prevented the development of emphysema in a chronic model of cigarette smoke exposure, while at 1 mg/kg was ineffective. Here we investigated the effects of roflumilast on the volume density (V<sub>V</sub>) of the inflammatory cells present in the lungs after chronic cigarette smoke exposure.</p> <p>Methods</p> <p>Slides were obtained from blocks of the previous study and V<sub>V </sub>was assessed immunohistochemically and by point counting using a grid with 48 points, a 20× objective and a computer screen for a final magnification of 580×. Neutrophils were marked with myeloperoxidase antibody, macrophages with Mac-3, dendritic cells with fascin, B-lymphocytes with B220, CD4+ T-cells with CD4+ antibody, and CD8+T-cells with CD8-α. The significance of the differences was calculated using one-way analysis of variance.</p> <p>Results</p> <p>Chronic smoke exposure increased neutrophil V<sub>V </sub>by 97%, macrophage by 107%, dendritic cell by 217%, B-lymphocyte by 436%, CD4+ by 524%, and CD8+ by 417%. The higher dose of roflumilast prevented the increase in neutrophil V<sub>V </sub>by 78%, macrophage by 82%, dendritic cell by 48%, B-lymphocyte by 100%, CD4+ by 98% and CD8+ V<sub>V </sub>by 88%. The lower dose of roflumilast did not prevent the increase in neutrophil, macrophage and B-cell V<sub>V </sub>but prevented dendritic cells by 42%, CD4+ by 55%, and CD8+ by 91%.</p> <p>Conclusion</p> <p>These results indicate (<it>i</it>) chronic exposure to cigarette smoke in mice results in a significant recruitment into the lung of inflammatory cells of both the innate and adaptive immune system; (<it>ii</it>) roflumilast at the higher dose exerts a protective effect against the recruitment of all these cells and at the lower dose against the recruitment of dendritic cells and T-lymphocytes; (<it>iii</it>) these findings underline the role of innate immunity in the development of pulmonary emphysema and (<it>iiii</it>) support previous results indicating that the inflammatory cells of the adaptive immune system do not play a central role in the development of cigarette smoke induced emphysema in mice.</p
Circulating mediators of inflammation and immune activation in AIDS-related non-Hodgkin lymphoma
Background: Non-Hodgkin lymphoma (NHL) is the most common AIDS-related malignancy in developed countries. An elevated risk of developing NHL persists among HIV-infected individuals in comparison to the general population despite the advent of effective antiretroviral therapy. The mechanisms underlying the development of AIDS-related NHL (A-NHL) are not fully understood, but likely involve persistent B-cell activation and inflammation. Methods: This was a nested case-control study within the ongoing prospective Multicenter AIDS Cohort Study (MACS). Cases included 47 HIV-positive male subjects diagnosed with high-grade B-cell NHL. Controls were matched to each case from among participating HIV-positive males who did not develop any malignancy. Matching criteria included time HIV+ or since AIDS diagnosis, age, race and CD4+ cell count. Sera were tested for 161 serum biomarkers using multiplexed beadbased immunoassays. Results: A subset of 17 biomarkers, including cytokines, chemokines, acute phase proteins, tissue remodeling agents and bone metabolic mediators was identified to be significantly altered in A-NHL cases in comparison to controls. Many of the biomarkers included in this subset were positively correlated with HIV viral load. A pathway analysis of our results revealed an extensive network of interactions between current and previously identified biomarkers. Conclusions: These findings support the current hypothesis that A-NHL develops in the context of persistent immune stimulation and inflammation. Further analysis of the biomarkers identified in this report should enhance our ability to diagnose, monitor and treat this disease. © 2014 Nolen et al
Statistical Epistasis and Functional Brain Imaging Support a Role of Voltage-Gated Potassium Channels in Human Memory
Despite the current progress in high-throughput, dense genome scans, a major portion of complex traits' heritability still remains unexplained, a phenomenon commonly termed “missing heritability.” The negligence of analytical approaches accounting for gene-gene interaction effects, such as statistical epistasis, is probably central to this phenomenon. Here we performed a comprehensive two-way SNP interaction analysis of human episodic memory, which is a heritable complex trait, and focused on 120 genes known to show differential, memory-related expression patterns in rat hippocampus. Functional magnetic resonance imaging was also used to capture genotype-dependent differences in memory-related brain activity. A significant, episodic memory-related interaction between two markers located in potassium channel genes (KCNB2 and KCNH5) was observed (Pnominal combined = 0.000001). The epistatic interaction was robust, as it was significant in a screening (Pnominal = 0.0000012) and in a replication sample (Pnominal = 0.01). Finally, we found genotype-dependent activity differences in the parahippocampal gyrus (Pnominal = 0.001) supporting the behavioral genetics finding. Our results demonstrate the importance of analytical approaches that go beyond single marker statistics of complex traits
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