MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Exact solution of the Zeeman effect in single-electron systems

Contrary to popular belief, the Zeeman effect can be treated exactly in single-electron systems, for arbitrary magnetic field strengths, as long as the term quadratic in the magnetic field can be ignored. These formulas were actually derived already around 1927 by Darwin, using the classical picture of angular momentum, and presented in their proper quantum-mechanical form in 1933 by Bethe, although without any proof. The expressions have since been more or less lost from the literature; instead, the conventional treatment nowadays is to present only the approximations for weak and strong fields, respectively. However, in fusion research and other plasma physics applications, the magnetic fields applied to control the shape and position of the plasma span the entire region from weak to strong fields, and there is a need for a unified treatment. In this paper we present the detailed quantum-mechanical derivation of the exact eigenenergies and eigenstates of hydrogen-like atoms and ions in a static magnetic field. Notably, these formulas are not much more complicated than the better-known approximations. Moreover, the derivation allows the value of the electron spin gyromagnetic ratio $g_s$ to be different from 2. For completeness, we then review the details of dipole transitions between two hydrogenic levels, and calculate the corresponding Zeeman spectrum. The various approximations made in the derivation are also discussed in details.Comment: 18 pages, 4 figures. Submitted to Physica Script

Spaceborne radar observations: A guide for Magellan radar-image analysis

Geologic analyses of spaceborne radar images of Earth are reviewed and summarized with respect to detecting, mapping, and interpreting impact craters, volcanic landforms, eolian and subsurface features, and tectonic landforms. Interpretations are illustrated mostly with Seasat synthetic aperture radar and shuttle-imaging-radar images. Analogies are drawn for the potential interpretation of radar images of Venus, with emphasis on the effects of variation in Magellan look angle with Venusian latitude. In each landform category, differences in feature perception and interpretive capability are related to variations in imaging geometry, spatial resolution, and wavelength of the imaging radar systems. Impact craters and other radially symmetrical features may show apparent bilateral symmetry parallel to the illumination vector at low look angles. The styles of eruption and the emplacement of major and minor volcanic constructs can be interpreted from morphological features observed in images. Radar responses that are governed by small-scale surface roughness may serve to distinguish flow types, but do not provide unambiguous information. Imaging of sand dunes is rigorously constrained by specific angular relations between the illumination vector and the orientation and angle of repose of the dune faces, but is independent of radar wavelength. With a single look angle, conditions that enable shallow subsurface imaging to occur do not provide the information necessary to determine whether the radar has recorded surface or subsurface features. The topographic linearity of many tectonic landforms is enhanced on images at regional and local scales, but the detection of structural detail is a strong function of illumination direction. Nontopographic tectonic lineaments may appear in response to contrasts in small-surface roughness or dielectric constant. The breakpoint for rough surfaces will vary by about 25 percent through the Magellan viewing geometries from low to high Venusian latitudes. Examples of anomalies and system artifacts that can affect image interpretation are described

The Diffuse Gamma-Ray Background from Supernovae

The Cosmic Gamma-ray Background (CGB) in the MeV region is believed to be due to photons from radioactivity produced in SNe throughout the history of galaxies in the universe. In particular, gamma-ray line emission from the decay chain 56Ni-> 56Co->56Fe provides the dominant photon source. Although iron synthesis occurs in all types of SNe, the contribution to the CGB is dominated by SNIa events due to their higher photon escape probabilities. Estimates of the star formation history in the universe suggest a rapid increase by a factor \~ 10 from the present to a redshift z_p ~ 1.5, beyond which it either remains constant or decreases slowly. We integrate the observed star formation history to determine the CGB from the corresponding SN rate history. In addition to gamma-rays from short-lived radioactivity in SNIa and SNII/Ibc we also calculate the minor contributions from long-lived radioactivities (26Al, 44Ti, 60Co, and electron-positron pair annihilation). Although progenitor evolution for SNIa is not yet fully understood, various arguments suggest delays of order 1-2 Gy between star formation and the production of SNIa's. The effect of this delay on the CGB is discussed. We emphasize the value of gamma-ray observations of the CGB in the MeV range as an independent tool for studies of the cosmic star formation history. If the delay between star formation and SNIa activity exceeds 1 Gy substantially, and/or the peak of the cosmic star formation rate occurs at a redshift much larger than unity, the gamma-ray production of SNIa would be insufficient to explain the observed CGB. Alternatively, the cosmic star formation rate would have to be higher (by a factor 2-3) than commonly assumed, which is in accord with several upward revisions reported in the recent literature.Comment: Minor changes, 26 pages, 9 figures, Accepted by Ap

How artists working in academia view artistic practice as research: Implications for tertiary music education

Artistic research output struggles for recognition as ‘legitimate’ research within the highly competitive and often traditional university sector. Often recognition requires the underpinning processes and thinking to be documented in a traditional written format. This article discusses the views of eight arts practitioners working in academia by asking whether or not they view their arts practice as research; and if they do, how it is so. The findings illuminate ways in which artistic practice is understood as research and reveal how the process of analytical and reflective writing impacts artist academics, their artistic and academic identities and their environment. The findings suggest a frame within which to advocate the equivalence of artistic research with traditional scholarly research. They also suggest a rationale for arguing against this, focusing instead (or perhaps as well) on a wider understanding of what constitutes knowledge. This has implications for academics, for students and for universities in recognising the research inherent within arts practice itself, and in recognising the value of practice-led writing in understanding and communicating new knowledge, new methods, and new definitions of research

Diffuse Gamma-Ray Emission from Starburst Galaxies and M31

We present a search for high energy gamma-ray emission from 9 nearby starburst galaxies and M31 with the EGRET instrument aboard CGRO. Though the diffuse gamma-ray emission from starburst galaxies was suspected to be detectable, we find no emission from NGC 253, M82 nor from the average of all 9 galaxies. The 2 sigma upper limit for the EGRET flux above 100 MeV for the averaged survey observations is 1.8 x 10-8 ph cm-2 s-1. From a model of the expected radio and gamma-ray emission, we find that the magnetic field in the nuclei of these galaxies is > 25 micro Gauss, and the ratio of proton and electron densities is < 400. The EGRET limits indicate that the rate of massive star formation in the survey galaxies is only about an order of magnitude higher than in the Milky Way. The upper limit to the gamma-ray flux above 100 MeV for M31 is 1.6 x 10-8 ph cm-2 s-1. At the distance of M31, the Milky Way flux would be over twice this value, indicating higher gamma-ray emissivities in our Galaxy. Therefore, since the supernova rate of the Milky Way is higher than in M31, our null detection of M31 supports the theory of the supernova origin of cosmic rays in galaxies.Comment: 17 pages, plus 1 Postscript figure, AAS Latex macros v4.0, accepted for publication in ApJ Main Journa

Approximate probabilistic verification of hybrid systems

Hybrid systems whose mode dynamics are governed by non-linear ordinary differential equations (ODEs) are often a natural model for biological processes. However such models are difficult to analyze. To address this, we develop a probabilistic analysis method by approximating the mode transitions as stochastic events. We assume that the probability of making a mode transition is proportional to the measure of the set of pairs of time points and value states at which the mode transition is enabled. To ensure a sound mathematical basis, we impose a natural continuity property on the non-linear ODEs. We also assume that the states of the system are observed at discrete time points but that the mode transitions may take place at any time between two successive discrete time points. This leads to a discrete time Markov chain as a probabilistic approximation of the hybrid system. We then show that for BLTL (bounded linear time temporal logic) specifications the hybrid system meets a specification iff its Markov chain approximation meets the same specification with probability $1$. Based on this, we formulate a sequential hypothesis testing procedure for verifying -approximately- that the Markov chain meets a BLTL specification with high probability. Our case studies on cardiac cell dynamics and the circadian rhythm indicate that our scheme can be applied in a number of realistic settings

GATA2 haploinsufficient patients lack innate lymphoid cells that arise after hematopoietic cell transplantation.

Innate lymphoid cells (ILC) are important barrier tissue immune regulators. They play a pivotal role in early non-specific protection against infiltrating pathogens, regulation of epithelial integrity, suppression of pro-inflammatory immune responses and shaping the intestinal microbiota. GATA2 haploinsufficiency causes an immune disorder that is characterized by bone marrow failure and (near) absence of monocytes, dendritic cells, B cells and natural killer (NK) cells. T cells develop normally, albeit at lower numbers. Here, we describe the absence of ILCs and their progenitors in blood and bone marrow of two patients with GATA2 haploinsufficiency and show that all subsets of ILCs appear after allogeneic hematopoietic stem cell transplantation, irrespective of the preparative conditioning regimen. Our data indicate that GATA2 is involved in the development of hematopoietic precursor cells (HPC) towards the ILC lineage

Abrupt appearance of the domain pattern and fatigue of thin ferroelectric films

We study the domain structure in ferroelectric thin films with a `passive' layer (material with damaged ferroelectric properties) at the interface between the film and electrodes within a continuous medium approximation. An abrupt transition from a monodomain to a polydomain state has been found with the increase of the `passive' layer thickness $d$. The domain width changes very quickly at the transition (exponentially with $d^{-2}$). We have estimated the dielectric response $dP/dE$ (the slope of the hysteresis loop) in the `fatigued' multidomain state and found that it is in agreement with experiment, assuming realistic parameters of the layer. We derive a simple universal relation for the dielectric response, which scales as $1/d$, involving only the properties of the passive layer. This relation qualitatively reproduces the evolution of the hysteresis loop in fatigued samples and it could be tested with controlled experiments. It is expected that the coercive field should increase with decreasing lateral size of the film. We believe that specific properties of the domain structure under bias voltage in ferroelectrics with a passive layer can resolve the long-standing `paradox of the coercive field'.Comment: 5 pages, REVTeX 3.1 with two eps-figures. Minor amendments. To appear in Phys. Rev. Letter