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.

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

Mast cells, eosinophils and IgE-positive cells in the nasal mucose of patients with vasomotor rhinitis - An immunohistochemical study

Vasomotor rhinitis (VMR) is a disorder of unknown pathogenesis. Forty patients with VMR were carefully selected on the basis of inclusion and exclusion criteria proposed by Mygind and Weeke. Nasal biopsy specimens were taken in the patient group as well as in a group of ten controls. Brush cytology was also taken in the VMR group. Inflammatory cells were identified and counted in the nasal mucosa, with the use of immunohistochemical techniques and a panel of monoclonal antibodies. Eosinophils were studied with the use of BMK13, EG2, and Giemsa. Mast cells were studied with anti-chymase (B7), anti-tryptase (G3) and toluidine blue. Sections were stained with IgE as well. There was no significant difference in the number of eosinophils, mast cells and IgE-positive cells between the two groups. Additionally, in contrast with other reports, in sections that were double-stained with anti-chymase and anti-tryptase, single chymase-positive cells were found

The effect of nasal steroid aqueous spray on nasal complaint scores and cellular infiltrates in the nasal mucosa of patients with nonallergic, noninfectious perennial rhinitis

Topical corticosteroids are the therapy of choice for nonallergic, noninfectious perennial rhinitis (NANIPER). However, the efficacy of steroid therapy in NANIPER is controversial, as is its mode of action. To our surprise, of 300 patients initially diagnosed as having NANIPER, only 65 reached threshold nasal symptom scores. Patients were randomized into four different treatment regimens: placebo administered twice daily (BD) for 8 weeks, fluticasone propionate aqueous nasal spray (FPANS) (200 microg) once daily (OD) and placebo OD for 8 weeks, FPANS (200 microg) OD and placebo OD for 4 weeks followed by FPANS (200 microg) BD for 4 weeks, and FPANS (200 microg) BD for 8 weeks. A small decrease in nasal symptoms was found, which only reached significance for sneezing in the FPANS 200 microg BD group. A significant dose-dependent decrease in immunocompetent cells was found in nasal biopsy specimens obtained before, after 4 weeks, and after 8 weeks of treatment. We conclude that FPANS did not significantly reduce nasal symptoms in this group of selected NANIPER patients, even though a significant effect on cells in the nasal mucosa was see

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

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

Probing photo-ionization: Experiments on positive streamers in pure gasses and mixtures

Positive streamers are thought to propagate by photo-ionization whose parameters depend on the nitrogen:oxygen ratio. Therefore we study streamers in nitrogen with 20%, 0.2% and 0.01% oxygen and in pure nitrogen, as well as in pure oxygen and argon. Our new experimental set-up guarantees contamination of the pure gases to be well below 1 ppm. Streamers in oxygen are difficult to measure as they emit considerably less light in the sensitivity range of our fast ICCD camera than the other gasses. Streamers in pure nitrogen and in all nitrogen/oxygen mixtures look generally similar, but become somewhat thinner and branch more with decreasing oxygen content. In pure nitrogen the streamers can branch so much that they resemble feathers. This feature is even more pronounced in pure argon, with approximately 10^2 hair tips/cm^3 in the feathers at 200 mbar; this density could be interpreted as the free electron density creating avalanches towards the streamer stem. It is remarkable that the streamer velocity is essentially the same for similar voltage and pressure in all nitrogen/oxygen mixtures as well as in pure nitrogen, while the oxygen concentration and therefore the photo-ionization lengths vary by more than five orders of magnitude. Streamers in argon have essentially the same velocity as well. The physical similarity of streamers at different pressures is confirmed in all gases; the minimal diameters are smaller than in earlier measurements.Comment: 28 pages, 14 figures. Major differences with v1: - appendix and spectra removed - subsection regarding effects of repetition frequency added - many more smaller change

An all silicon quantum computer

A solid-state implementation of a quantum computer composed entirely of silicon is proposed. Qubits are Si-29 nuclear spins arranged as chains in a Si-28 (spin-0) matrix with Larmor frequencies separated by a large magnetic field gradient. No impurity dopants or electrical contacts are needed. Initialization is accomplished by optical pumping, algorithmic cooling, and pseudo-pure state techniques. Magnetic resonance force microscopy is used for readout. This proposal takes advantage of many of the successful aspects of solution NMR quantum computation, including ensemble measurement, RF control, and long decoherence times, but it allows for more qubits and improved initialization.Comment: ReVTeX 4, 5 pages, 2 figure

Issues in Vendor/Library Relations-The Sales Call

We re-take a coding theoretic notion which goes back to Cl. Shannon: codeword distinguishability. This notion is standard in zero-error information theory, but its bearing is definitely wider and it may help to better understand new forms of coding, e.g. DNA word design. In our approach, the underlying decoding principle is very simple and very general: one decodes by trying to minimise the diversity (in the simplest case the Hamming distance) between a codeword and the output sequence observed at the end of the noisy transmission channel. Symmetrically and equivalently, one may use maximum-similarity decoders and and codeword confusabilities. The operational meaning of codewoord distinguishability is made clear by a reliability criterion, which generalises the well-known criterion on minimum Hamming distance for error-correcting codes. We investigate the formal properties of distinguishabilities versus diversities; these two notions are deeply related, and yet essentially different. An encoding theorem is put forward; as a case study we examine a channel of cryptographic interest