Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test

We present a novel approach to detect potential cis-acting regulatory loci that combines the functional potential, an empirical DNase-seq based estimate of the allele-specificity of DNase-I hypersensitivity sites, with kernel-based variance component association analyses against expression phenotypes. To test our method we used public ENCODE whole genome DNase-I sequencing data, from a single sample, to estimate the functional potentials of the subset of 10,552 noncoding heterozygous single-nucleotide polymorphisms (SNPs) that were also present in the Genetic Analysis Workshop 19 (GAW19) family-based data set. We then built two covariance kernels, one nonweighted and one weighted by the functional potentials, and conducted kernel-based variance component association analyses against the 20,527 transcript expression phenotypes in the GAW19 family-based data set. We found signals of potential cis-regulatory effects, that surpassed the Bonferroni significance threshold, for ten transcripts. Stepwise removal of the cis-located SNPs from the weighted kernel lead to the disappearance of the association signal from our top transcript hit. We found compelling evidence of allele-specific cis-regulation for four transcripts using both kernels, and our results agree with previous research that suggests the involvement of specific cis-located variants in the regulation of their neighboring gene

Acute effects of aerobic exercise on cognitive function in individuals with Parkinson’s disease

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.neulet.2018.01.056 © 2018. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/by-nc-nd/4.0/Deficits in executive functions are highly prevalent in Parkinson’s disease (PD). Although chronic physical exercise has been shown to improve executive functions in PD, evidence of acute exercise effects is limited. This study aimed to evaluate the effects of an acute bout of exercise on cognitive processes underlying executive functions in PD. Twenty individuals with PD were assessed in both a Control and an Exercise conditions. In each condition, individuals started performing a simple and a choice reaction time (RT) task. Subsequently, participants were asked to sit on a cycle ergometer (Control) or cycle (Exercise) for 20 min in counterbalanced order. Participants were asked to repeat both reaction time tasks after 15-min rest period in both conditions. While no differences were found in simple RT, participants showed faster choice RT post Exercise as well as Control conditions (p = .012). Participants had slower choice RT for target stimulus compared to non-target stimuli irrespective of time or experimental condition (p < .001). There was no change in accuracy following experimental conditions. Results suggest that individuals with PD may not respond behaviourally to a single bout of exercise. The lack of selective effects of exercise on cognition suggests that practice effects may have influenced previous research. Future studies should assess whether neurophysiological changes might occur after an acute bout of exercise in PD

On the difference of torus geometry between hidden and non-hidden broad line active galactic nuclei

We present results from the fitting of infrared (IR) spectral energy distributions of 21 active galactic nuclei (AGN) with clumpy torus models. We compiled high spatial resolution ($\sim 0.3$--$0.7$ arcsec) mid-IR $N$-band spectroscopy, $Q$-band imaging and nuclear near- and mid-IR photometry from the literature. Combining these nuclear near- and mid-IR observations, far-IR photometry and clumpy torus models, enables us to put constraints on the torus properties and geometry. We divide the sample into three types according to the broad line region (BLR) properties; type-1s, type-2s with scattered or hidden broad line region (HBLR) previously observed, and type-2s without any published HBLR signature (NHBLR). Comparing the torus model parameters gives us the first quantitative torus geometrical view for each subgroup. We find that NHBLR AGN have smaller torus opening angles and larger covering factors than those of HBLR AGN. This suggests that the chance to observe scattered (polarized) flux from the BLR in NHBLR could be reduced by the dual effects of (a) less scattering medium due to the reduced scattering volume given the small torus opening angle and (b) the increased torus obscuration between the observer and the scattering region. These effects give a reasonable explanation for the lack of observed HBLR in some type-2 AGN.Comment: 13 pages, 5 figures, accepted for publication in Ap

Differences between CO- and calcium triplet-derived velocity dispersions in spiral galaxies: evidence for central star formation?

We examine the stellar velocity dispersions (sigma) of a sample of 48 galaxies, 35 of which are spirals, from the Palomar nearby galaxy survey. It is known that for ultra-luminous infrared galaxies (ULIRGs) and merger remnants thesigma derived from the near-infrared CO band-heads is smaller than that measured from optical lines, while no discrepancy between these measurements is found for early-type galaxies. No such studies are available for spiral galaxies - the subject of this paper. We used cross-dispersed spectroscopic data obtained with the Gemini Near-Infrared Spectrograph (GNIRS), with spectral coverage from 0.85 to 2.5um, to obtain sigma measurements from the 2.29 $\mu$m CO band-heads (sigma_{CO}), and the 0.85 um calcium triplet (sigma_{CaT}). For the spiral galaxies in the sample, we found that sigma_{CO} is smaller than sigma_{CaT}, with a mean fractional difference of 14.3%. The best fit to the data is given by sigma_{opt} = (46.0+/-18.1) + (0.85+/-0.12)sigma_{CO}. This "sigma discrepancy" may be related to the presence of warm dust, as suggested by a slight correlation between the discrepancy and the infrared luminosity. This is consistent with studies that have found no sigma-discrepancy in dust-poor early-type galaxies, and a much larger discrepancy in dusty merger remnants and ULIRGs. That sigma_{CO}$ is lower than sigma_{opt} may also indicate the presence of a dynamically cold stellar population component. This would agree with the spatial correspondence between low sigma_{CO} and young/intermediate-age stellar populations that has been observed in spatially-resolved spectroscopy of a handful of galaxies.Comment: Published in MNRAS, 446, 282

Common Representation of Information Flows for Dynamic Coalitions

We propose a formal foundation for reasoning about access control policies within a Dynamic Coalition, defining an abstraction over existing access control models and providing mechanisms for translation of those models into information-flow domain. The abstracted information-flow domain model, called a Common Representation, can then be used for defining a way to control the evolution of Dynamic Coalitions with respect to information flow

Vers un changement de pratique dans une filière céréalière : apport de la modélisation de l’environnement

National audienceProject management, especially in the field of sustainable development, requires to take into account not only the working environment stricto sensu, but also supra components of environmental, social, economic, legislative, etc. Ergonomists and psychologists are then led to be interested in, and to develop modeling frameworks to better understand and to make more intelligible this complex environment. The study presented here, which requires taking into account this environment, aims at setting up a novel practice for improving the food safety of a cereal chain in a global context of sustainable development: protection of the environment (flora and fauna) and the health of farmers and consumers. As part of this study, a quick fungal contamination diagnostic tool and a corresponding decontamination process have been developed for an application in the barley-malt-beer food chain. However, the use of these processes may change the agricultural practices in antifungal treatments with the regular and high dose treatments replaced by fine targeted applications only where and when necessary. In relation with this technological development, the challenge is to identify the components of the environment that may become brakes and levers to the implementation of this new practice. In this scope, this investigation mobilizes the modeling of the environment of Thatcher and Yeow (2016). This paper is consequently aimed at presenting the underlying process to this construction, and this in relation with the characteristics of the study. At last, a discussion is initiated concerning the further use of such modelling practices for purposes other than the decision-making processes on ergonomic intervention purposes.L’intervention ergonomique dans le champ du développement durable requiert la prise en compte d’un environnement dépassant largement l’environnement de travail afin d’y intégrer des composants relevant de dimensions environnementales, économique, législative, etc. Les ergonomes et psychologues ergonomes sont alors conduits à développer des cadres de modélisation permettant d’appréhender et de rendre davantage intelligible cet environnement complexe. L’étude sur laquelle nous nous basons ici s’inscrit dans ce cadre et vise l’identification des freins et leviers à la mise en place d’une nouvelle pratique en matière de traitement antifongique pour la filière orge-malt-bière. Pour cette investigation, nous nous référons notamment à la modélisation de Thatcher et Yeow (2016). L’enjeu est de présenter le processus de recueil et d’analyse sous-jacente à la modélisation et de poursuivre par une réflexion quant à l’emploi de ces formes de modélisation au cours d’un processus d’intervention

Less than 10 percent of star formation in z=0.6 massive galaxies is triggered by major interactions

Both observations and simulations show that major tidal interactions or mergers between gas-rich galaxies can lead to intense bursts of starformation. Yet, the average enhancement in star formation rate (SFR) in major mergers and the contribution of such events to the cosmic SFR are not well estimated. Here we use photometric redshifts, stellar masses and UV SFRs from COMBO-17, 24 micron SFRs from Spitzer and morphologies from two deep HST cosmological survey fields (ECDFS/GEMS and A901/STAGES) to study the enhancement in SFR as a function of projected galaxy separation. We apply two-point projected correlation function techniques, which we augment with morphologically-selected very close pairs (separation <2 arcsec) and merger remnants from the HST imaging. Our analysis confirms that the most intensely star-forming systems are indeed interacting or merging. Yet, for massive (M* > 10^10 Msun) star-forming galaxies at 0.4<z<0.8, we find that the SFRs of galaxies undergoing a major interaction (mass ratios <1:4 and separations < 40 kpc) are only 1.80 +/- 0.30 times higher than the SFRs of non-interacting galaxies when averaged over all interactions and all stages of the interaction, in good agreement with other observational works. We demonstrate that these results imply that <10% of star formation at 0.4 < z < 0.8 is triggered directly by major mergers and interactions; these events are not important factors in the build-up of stellar mass since z=1.Comment: Submitted to ApJ. 41 pages, 11 figure