Literature-based priors for gene regulatory networks

Motivation: The use of prior knowledge to improve gene regulatory network modelling has often been proposed. In this paper we present the first research on the massive incorporation of prior knowledge from literature for Bayesian network learning of gene networks. As the publication rate of scientific papers grows, updating online databases, which have been proposed as potential prior knowledge in past rese-arch, becomes increasingly challenging. The novelty of our approach lies in the use of gene-pair association scores that describe the over-lap in the contexts in which the genes are mentioned, generated from a large database of scientific literature, harnessing the information contained in a huge number of documents into a simple, clear format. Results: We present a method to transform such literature-based gene association scores to network prior probabilities, and apply it to learn gene sub-networks for yeast, E. coli and Human organisms. We also investigate the effect of weighting the influence of the prior know-ledge. Our findings show that literature-based priors can improve both the number of true regulatory interactions present in the network and the accuracy of expression value prediction on genes, in comparison to a network learnt solely from expression data. Networks learnt with priors also show an improved biological interpretation, with identified subnetworks that coincide with known biological pathways. Contact

Enhancing Practice and Achievement in Introductory Programming With a Robot Olympics

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Temperature effects on the 15-85 mu m spectra of olivines and pyroxenes

Far-infrared spectra of laboratory silicates are normally obtained at room temperature even though the grains responsible for astronomical silicate emission bands seen at wavelengths >20 μm are likely to be at temperatures below ∼150 K. In order to investigate the effect of temperature on silicate spectra, we have obtained absorption spectra of powdered forsterite and olivine, along with two orthoenstatites and diopside clinopyroxene, at 3.5±0.5 K and at room temperature (295±2 K). To determine the changes in the spectra the resolution must be increased from ∼1 to 0.25 cm−1 at both temperatures, because a reduction in temperature reduces the phonon density, thereby reducing the width of the infrared peaks. Several bands observed at 295 K split at 3.5 K. At 3.5 K the widths of isolated single bands in olivine, enstatites and diopside are ∼90 per cent of their 295-K widths. However, in forsterite the 3.5-K widths of the 31-, 49- and 69-μm bands are, respectively, 90, 45 and 31 per cent of their 295-K widths. Owing to an increase in phonon energy as the lattice contracts, 3.5-K singlet peaks occur at shorter wavelengths than do the corresponding 295-K peaks; the magnitude of the wavelength shift increases from ∼0–0.2 μm at 25 μm to ∼0.9 μm at 80 μm. In olivines and enstatites the wavelength shifts can be approximated by polynomials of the form ax+bx2 where x=λpk(295 K) and the coefficients a and b differ between minerals; for diopside this formula gives a lower limit to the shift. Changes in the relative absorbances of spectral peaks are also observed. The temperature dependence of λpk and bandwidth shows promise as a means to deduce characteristic temperatures of mineralogically distinct grain populations. In addition, the observed changes in band strength with temperature will affect estimates of grain masses and relative mineral abundances inferred using room-temperature laboratory data. Spectral measurements of a variety of minerals at a range of temperatures are required to quantify these effects fully

Let me Google that for you:a time series analysis of seasonality in internet search trends for terms related to foot and ankle pain

BACKGROUND: The analysis of internet search traffic may present the opportunity to gain insights into general trends and patterns in information seeking behaviour related to medical conditions at a population level. For prevalent and widespread problems such as foot and ankle pain, this information has the potential to improve our understanding of seasonality and trends within these conditions and their treatments, and may act as a useful proxy for their true incidence/prevalence characteristics. This study aimed to explore seasonal effects, general trends and relative popularity of internet search terms related to foot and ankle pain over the past decade. METHODS: We used the Google Trends tool to obtain relative search engine traffic for terms relating to foot and ankle pain and common treatments from Google search and affiliated pages for major northern and southern hemisphere English speaking nations. Analysis of overall trends and seasonality including summer/winter differences was carried out on these terms. RESULTS: Searches relating to general foot pain were on average 3.4 times more common than those relating to ankle pain, and twice as common as searches relating to heel pain. Distinct seasonal effects were seen in the northern hemisphere, with large increases in search volumes in the summer months compared to winter for foot (p = 0.004, 95 % CI [22.2–32.1]), ankle (p = 0.0078, 95 % CI [20.9–35.5]), and heel pain (p = 0.004, 95 % CI [29.1–45.6]). These seasonal effects were reflected by data from Australia, with the exception of ankle pain. Annual seasonal effects for treatment options were limited to terms related to foot surgery and ankle orthoses (p = 0.031, 95 % CI [3.5–20.9]; p = 0.004, 95 % CI [7.6–25.2] respectively), again increasing in the summer months. CONCLUSIONS: A number of general trends and annual seasonal effects were found in time series internet search data for terms relating to foot and ankle pain. This data may provide insights into these conditions at population levels. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13047-015-0074-9) contains supplementary material, which is available to authorized users

Simulating Reionization: Character and Observability

In recent years there has been considerable progress in our understanding of the nature and properties of the reionization process. In particular, the numerical simulations of this epoch have made a qualitative leap forward, reaching sufficiently large scales to derive the characteristic scales of the reionization process and thus allowing for realistic observational predictions. Our group has recently performed the first such large-scale radiative transfer simulations of reionization, run on top of state-of-the-art simulations of early structure formation. This allowed us to make the first realistic observational predictions about the Epoch of Reionization based on detailed radiative transfer and structure formation simulations. We discuss the basic features of reionization derived from our simulations and some recent results on the observational implications for the high-redshift Ly-alpha sources.Comment: 3 pages, to appear in the Proceedings of First Stars III, Santa Fe, July 2007, AIP Conference Serie

The 69-mu m forsterite band as a dust temperature indicator

A band of pure crystalline forsterite (100 per cent Mg2SiO4) occurs at 69.67 μm at room temperature (295 K); for olivines with ≳10 per cent Fe the corresponding feature is at ≳73 μm. The Mg-rich forsterite feature is observed in a variety of ISO LWS spectra, but the corresponding Fe-rich olivine feature is not. For the 10 astronomical sources in our sample, the forsterite band peaks in the 68.9–69.3 μm range and narrows with decreasing peak wavelength. This is consistent with the shortwards shifting of the peak observed when laboratory samples are cooled to 77 K (69.07 μm) and 3.5 K (68.84 μm). The shifted peak is produced by lattice contraction and the sharpening is due to a decrease in phonon density at lower temperatures. However, the astronomical bands are narrower than those of the laboratory samples. By comparing the laboratory and astronomical peak wavelengths, we deduce characteristic forsterite 69-μm band temperatures that are in the 27–84 K range for the eight post-main-sequence objects in our sample. These values are shown to be consistent with the local continuum temperatures derived using a β=1.5 dust emissivity index, similar to derived interstellar values of the opacity index. For the pre-main sequence-objects HD 100546 and MWC 922, the characteristic 69-μm forsterite band temperatures (127±18 and 139±10 K, respectively) are significantly higher than those of the post-main-sequence objects and are more than twice as high as their local continuum temperatures deduced using β=1.5. The assumption of large grains (β=0) can produce agreement between the derived 69-μm and continuum temperatures for one of these objects but not for the other — a spatial separation between the forsterite and continuum-emitting grains may therefore be implied for it. We conclude that observations of the peak wavelength and FWHM of the 69-μm forsterite band show great promise as a new diagnostic of characteristic grain temperatures

Increased NBCn1 expression, Na+/HCO3- co-transport and intracellular pH in human vascular smooth muscle cells with a risk allele for hypertension.

Genome-wide association studies have revealed an association between variation at the SLC4A7 locus and blood pressure. SLC4A7 encodes the electroneutral Na+/HCO3- co-transporter NBCn1 which regulates intracellular pH (pHi). We conducted a functional study of variants at this locus in primary cultures of vascular smooth muscle and endothelial cells. In both cell types, we found genotype-dependent differences for rs13082711 in DNA-nuclear protein interactions, where the risk allele is associated with increased SLC4A7 expression level, NBCn1 availability and function as reflected in elevated steady-state pHi and accelerated recovery from intracellular acidosis. However, in the presence of Na+/H+ exchange activity, the SLC4A7 genotypic effect on net base uptake and steady-state pHi persisted only in vascular smooth muscle cells but not endothelial cells. We found no discernable effect of the missense polymorphism resulting in the amino acid substitution Glu326Lys. The finding of a genotypic influence on SLC4A7 expression and pHi regulation in vascular smooth muscle cells provides an insight into the molecular mechanism underlying the association of variation at the SLC4A7 locus with blood pressure

Vortices enable the complex aerobatics of peregrine falcons

The peregrine falcon (Falco peregrinus) is known for its extremely high speeds during hunting dives or stoop. Here we demonstrate that the superior manoeuvrability of peregrine falcons during stoop is attributed to vortex-dominated flow promoted by their morphology, in the M-shape configuration adopted towards the end of dive. Both experiments and simulations on life-size models, derived from field observations, revealed the presence of vortices emanating from the frontal and dorsal region due to a strong spanwise flow promoted by the forward sweep of the radiale. These vortices enhance mixing for flow reattachment towards the tail. The stronger wing and tail vortices provide extra aerodynamic forces through vortex-induced lift for pitch and roll control. A vortex pair with a sense of rotation opposite to that from conventional planar wings interacts with the main wings vortex to reduce induced drag, which would otherwise decelerate the bird significantly during pull-out. These findings could help in improving aircraft performance and wing suits for human flights

Ready Both to Your and to My Hands: Mapping the Action Space of Others

To date, mutual interaction between action and perception has been investigated mainly by focusing on single individuals. However, we perceive affording objects and acts upon them in a surrounding world inhabited by other perceiving and acting bodies. Thus, the issue arises as to whether our action-oriented object perception might be modulated by the presence of another potential actor. To tackle this issue we used the spatial alignment effect paradigm and systematically examined this effect when a visually presented handled object was located close either to the perceiver or to another individual (a virtual avatar). We found that the spatial alignment effect occurred whenever the object was presented within the reaching space of a potential actor, regardless of whether it was the participant's own or the other's reaching space. These findings show that objects may afford a suitable motor act when they are ready not only to our own hand but also, and most importantly, to the other's hand. Our proposal is that this effect is likely to be due to a mapping of our own and the other's reaching space and we posit that such mapping could play a critical role in joining our own and the other's action

Magnetic Fluffy Dark Matter

We explore extensions of inelastic Dark Matter and Magnetic inelastic Dark Matter where the WIMP can scatter to a tower of heavier states. We assume a WIMP mass $m_\chi \sim \mathcal{O}(1-100)$ GeV and a constant splitting between successive states $\delta \sim\mathcal{O}(1 - 100)$ keV. For the spin-independent scattering scenario we find that the direct experiments CDMS and XENON strongly constrain most of the DAMA/LIBRA preferred parameter space, while for WIMPs that interact with nuclei via their magnetic moment a region of parameter space corresponding to $m_{\chi}\sim 11$ GeV and $\delta < 15$ keV is allowed by all the present direct detection constraints.Comment: 16 pages, 6 figures, added comments about magnetic moment form factor to Sec 3.1.2 and results to Sec 3.2.2, final version to be published in JHE