The importance of detailed epigenomic profiling of different cell types within organs.

The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes

X-ray properties of UV-selected star forming galaxies at z~1 in the Hubble Deep Field North

We present an analysis of the X-ray emission from a large sample of ultraviolet (UV) selected, star forming galaxies with 0.74<z<1.32 in the Hubble Deep Field North (HDF-N) region. By excluding all sources with significant detected X-ray emission in the 2 Ms Chandra observation we are able to examine the properties of galaxies for which the emission in both UV and X-ray is expected to be predominantly due to star formation. Stacking the X-ray flux from 216 galaxies in the soft and hard bands produces significant detections. The derived mean 2-10 keV rest-frame luminosity is 2.97+/-0.26x10^(40) erg/s, corresponding to an X-ray derived star formation rate (SFR) of 6.0+/-0.6 Msolar/yr. Comparing the X-ray value with the mean UV derived SFR, uncorrected for attenuation, we find that the average UV attenuation correction factor is \~3. By binning the galaxy sample according to UV magnitude and colour, correlations between UV and X-ray emission are also examined. We find a strong positive correlation between X-ray emission and rest-frame UV emission. A correlation between the ratio of X-ray-to-UV emission and UV colour is also seen, such that L(X)/L(UV) increases for redder galaxies. Given that X-ray emission offers a view of star formation regions that is relatively unaffected by extinction, results such as these can be used to evaluate the effects of dust on the UV emission from high-z galaxies. For instance we derive a relationship for estimating UV attenuation corrections as a function of colour excess. The observed relation is inconsistent with the Calzetti et al. (2000) reddening law which over predicts the range in UV attenuation corrections by a factor of ~100 for the UV selected z~1 galaxies in this sample (abridged).Comment: 10 pages, 7 figures, accepted for publication in MNRA

Weighted-density approximation for general nonuniform fluid mixtures

In order to construct a general density-functional theory for nonuniform fluid mixtures, we propose an extension to multicomponent systems of the weighted-density approximation (WDA) of Curtin and Ashcroft [Phys. Rev. A 32, 2909 (1985)]. This extension corrects a deficiency in a similar extension proposed earlier by Denton and Ashcroft [Phys. Rev. A 42, 7312 (1990)], in that that functional cannot be applied to the multi-component nonuniform fluid systems with spatially varying composition, such as solid-fluid interfaces. As a test of the accuracy of our new functional, we apply it to the calculation of the freezing phase diagram of a binary hard-sphere fluid, and compare the results to simulation and the Denton-Ashcroft extension.Comment: 4 pages, 4 figures, to appear in Phys. Rev. E as Brief Repor

PG 1700+518 Revisited: Adaptive Optics Imaging and a Revised Starburst Age for the Companion

We present the results of adaptive-optics imaging of the z=0.2923 QSO PG 1700+518 in the J and H bands. The extension to the north of the QSO is clearly seen to be a discrete companion with a well-defined tidal tail, rather than a feature associated with the host galaxy of PG 1700+518 itself. On the other hand, an extension to the southwest of the QSO (seen best in deeper, but lower-resolution, optical images) does likely comprise tidal material from the host galaxy. The SED derived from images in J, H, and two non-standard optical bands indicates the presence of dust intermixed with the stellar component. We use our previously reported Keck spectrum of the companion, the SED found from the imaging data, and updated spectral-synthesis models to constrain the stellar populations in the companion and to redetermine the age of the starburst. While our best-fit age of 0.085 Gyr is nearly the same as our earlier determination, the fit of the new models is considerably better. This age is found to be remarkably robust with respect to different assumptions about the nature of the older stellar component and the effects of dust.Comment: 11 pages; includes two eps figures. Latex (AASTEX). Two additional figures in gif format. Postscript version including all figs. (424 kb) can be obtained from http://www.ifa.hawaii.edu/~canaguby/preprints.html To appear in ApJ. Letter

How People Reason about Temporal Relations

The paper describes a theory of temporal reasoning and its implementation in a computer program. The theory postulates that individuals construct mental models, and it predicts that inferences that call for only one model to be constructed, such as: a happens before b. b happens before c. d happens while b. e happens while c. What is the temporal relation between d and e? will be easier than those that call for multiple models, such as a problem identical to the previous one except for its first premise: a happens before c. Experiment 1 showed that subjects were faster and more accurate with one-model problems than with multiple-model problems. They look more time to read a premise leading to multiple models than the corresponding premise in a one-model problem. Experiment 2 showed that if the question came first and was presented with all the premises, then subjects can ignore an irrelevant premise. As predicted, the difference between one-model and multiple-model problems with valid conclusions then disappeared. Experiment 3 showed that the size of a model, i.e., the number of events in it, and the distance apart of the critical events, also affected performance

How to Make the Impossible Seem Probable

The mental model theory postulates that reasoners build models of the situations described in premises. A conclusion is possible if it occurs in at least one model; it is probable if occurs in most models; and it is necessary if it occurs in all models. The theory also postulates that reasoners represent as much information as possible in implicit models. Experiment 1 showed that, as predicted, conclusions about possible situations tend to correspond to explicit models rather than to implicit models. Experiment 2 yielded a discovery: there are illusory inferences with conclusions that seem plausible but that are in reality gross errors. In such cases, as the model theory predicts, subjects judge as the more probable of two events one that is impossible. For example, given that only one of the following two assertions is true: There is a king or an ace in the hand, or both. There is a queen or an ace in the hand, or both. subjects judge that the ace is more likely to be in the hand than the king. In fact, it is impossible for an ace to be in the hand

Negations in syllogistic reasoning: Evidence for a heuristic–analytic conflict

An experiment utilizing response time measures was conducted to test dominant processing strategies in syllogistic reasoning with the expanded quantifier set proposed by Roberts (2005). Through adding negations to existing quantifiers it is possible to change problem surface features without altering logical validity. Biases based on surface features such as atmosphere, matching, and the probability heuristics model (PHM; Chater & Oaksford, 1999; Wetherick & Gilhooly, 1995) would not be expected to show variance in response latencies, but participant responses should be highly sensitive to changes in the surface features of the quantifiers. In contrast, according to analytic accounts such as mental models theory and mental logic (e.g., Johnson-Laird & Byrne, 1991; Rips, 1994) participants should exhibit increased response times for negated premises, but not be overly impacted upon by the surface features of the conclusion. Data indicated that the dominant response strategy was based on a matching heuristic, but also provided evidence of a resource-demanding analytic procedure for dealing with double negatives. The authors propose that dual-process theories offer a stronger account of these data whereby participants employ competing heuristic and analytic strategies and fall back on a heuristic response when analytic processing fails