The evolution of galaxy groups and of galaxies therein

Properties of groups of galaxies depend sensitively on the algorithm for group selection, and even the most recent catalogs of groups built from redshift-space selection should suffer from projections and infalling galaxies. The cosmo-dynamical evolution of groups from initial Hubble expansion to collapse and virialization leads to a fundamental track (FT) in virial-theorem-M/L vs crossing time. The increased rates of mergers, both direct and after dynamical friction, in groups relative to clusters, explain the higher fraction of elliptical galaxies at given local number density in X-ray selected groups, relative to clusters, even when the hierarchical evolution of groups is considered. Galaxies falling into groups and clusters should later travel outwards to typically 2 virial radii, which is somewhat less than the outermost radius where observed galaxy star formation efficiencies are enhanced relative to field galaxies of same morphological type. An ongoing analysis of the internal kinematics of X-ray selected groups suggests that the radial profiles of line of sight velocity dispersion are consistent with isotropic NFW distributions for the total mass density, with higher (lower) concentrations than LambdaCDM predictions in groups of high (low) mass. The critical mass, at M200 ~ 10^13 M_sun is consistent with possible breaks in the X-ray luminosity-temperature and Fundamental Plane relations. The internal kinematics of groups indicate that the M-T relation of groups should agree with that extrapolated from clusters with no break at the group scale. The analyses of observed velocity dispersion profiles and of the FT both suggest that low velocity dispersion groups (compact and loose, X-ray emitting or undetected) are quite contaminated by chance projections.Comment: Invited review, ESO workshop "Groups of Galaxies in the Nearby Universe", held in Santiago, Chile, 5-9 December 2005, ed. I. Saviane, V. Ivanov & J. Borissova, 16 page

Resolving the Azimuthal Ambiguity in Vector Magnetogram Data with the Divergence-Free Condition: Application to Discrete Data

We investigate how the divergence-free property of magnetic fields can be exploited to resolve the azimuthal ambiguity present in solar vector magnetogram data, by using line-of-sight and horizontal heliographic derivative information as approximated from discrete measurements. Using synthetic data we test several methods that each make different assumptions about how the divergence-free property can be used to resolve the ambiguity. We find that the most robust algorithm involves the minimisation of the absolute value of the divergence summed over the entire field of view. Away from disk centre this method requires the sign and magnitude of the line-of-sight derivatives of all three components of the magnetic field vector.Comment: Solar Physics, in press, 20 pages, 11 figure

Functional and genomic analyses of α-solenoid proteins

{alpha}-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some {alpha}-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of {alpha}-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of {alpha}-solenoids. Unexpectedly, we identified occurrences of {alpha}-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known {alpha}-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that {alpha}-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of {alpha}-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that {alpha}-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of {alpha}-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

BACKGROUND: Biological knowledge is represented in scientific literature that often describes the function of genes/proteins (bioentities) in terms of their interactions (biointeractions). Such bioentities are often related to biological concepts of interest that are specific of a determined research field. Therefore, the study of the current literature about a selected topic deposited in public databases, facilitates the generation of novel hypotheses associating a set of bioentities to a common context. RESULTS: We created a text mining system (LAITOR: Literature Assistant for Identification of Terms co-Occurrences and Relationships) that analyses co-occurrences of bioentities, biointeractions, and other biological terms in MEDLINE abstracts. The method accounts for the position of the co-occurring terms within sentences or abstracts. The system detected abstracts mentioning protein-protein interactions in a standard test (BioCreative II IAS test data) with a precision of 0.82-0.89 and a recall of 0.48-0.70. We illustrate the application of LAITOR to the detection of plant response genes in a dataset of 1000 abstracts relevant to the topic. CONCLUSIONS: Text mining tools combining the extraction of interacting bioentities and biological concepts with network displays can be helpful in developing reasonable hypotheses in different scientific backgrounds

Dark Energy and Extending the Geodesic Equations of Motion: Its Construction and Experimental Constraints

With the discovery of Dark Energy, $\Lambda_{DE}$, there is now a universal length scale, $\ell_{DE}=c/(\Lambda_{DE} G)^{1/2}$, associated with the universe that allows for an extension of the geodesic equations of motion. In this paper, we will study a specific class of such extensions, and show that contrary to expectations, they are not automatically ruled out by either theoretical considerations or experimental constraints. In particular, we show that while these extensions affect the motion of massive particles, the motion of massless particles are not changed; such phenomena as gravitational lensing remain unchanged. We also show that these extensions do not violate the equivalence principal, and that because $\ell_{DE}=14010^{800}_{820}$ Mpc, a specific choice of this extension can be made so that effects of this extension are not be measurable either from terrestrial experiments, or through observations of the motion of solar system bodies. A lower bound for the only parameter used in this extension is set.Comment: 19 pages. This is the published version of the first half of arXiv:0711.3124v2 with corrections include

Design of an advanced intelligent instrument with waveform recognition based on the ITMS platform

Searching for similar behavior in previous data plays a key role in fusion research, but can be quite challenging to implement from a practical point of view. This paper describes the design of an intelligent measurement instrument that uses similar waveform recognition systems (SWRS) to extract knowledge from the signals it acquires. The system is perceived as an Ethernet measurement instrument that permits to acquire several waveforms simultaneously and to identity similar behaviors by searching in previous data using distributed SWRS. The implementation is another example of the advantages that local processing capabilities can provide in data acquisition applications

Dark matter halos and the anisotropy of ultra-high energy cosmic rays

Several explanations for the existence of Ultra High Energy Cosmic Rays invoke the idea that they originate from the decay of massive particles created in the reheating following inflation. It has been suggested that the decay products can explain the observed isotropic flux of cosmic rays. We have calculated the anisotropy expected for various models of the dark matter distribution and find that at present data are too sparse above $4 \times 10^{19}$ eV to discriminate between different models. However we show that with data from three years of operation of the southern section of the Pierre Auger Observatory significant progress in testing the proposals will be made.Comment: 21 pages, 6 figures (ps), Astroparticle Physics (accepted for publication

The clustering of ultra-high energy cosmic rays and their sources

The sky distribution of cosmic rays with energies above the 'GZK cutoff' holds important clues to their origin. The AGASA data, although consistent with isotropy, shows evidence for small-angle clustering, and it has been argued that such clusters are aligned with BL Lacertae objects, implicating these as sources. It has also been suggested that clusters can arise if the cosmic rays come from the decays of very massive relic particles in the Galactic halo, due to the expected clumping of cold dark matter. We examine these claims and show that both are in fact not justified.Comment: 13 pages, 8 figures, version in press at Phys. Rev.

An error tolerant memory aid for reduced cognitive load in number copying tasks

Number copying tasks are still common despite increased digitalization of services. Number copying tasks are cognitively and visually demanding, errors are easily introduced and the process is often perceived as laborious. This study proposes an alternative scheme based on dictionary coding that reduces the cognitive load on the user by a factor of five. The strategy has several levels of error detection and error correction characteristics and is easy to implemen

Non-linear numerical simulations of magneto-acoustic wave propagation in small-scale flux tubes

We present results of non-linear, 2D, numerical simulations of magneto-acoustic wave propagation in the photosphere and chromosphere of small-scale flux tubes with internal structure. Waves with realistic periods of three to five minutes are studied, after applying horizontal and vertical oscillatory perturbations to the equilibrium model. Spurious reflections of shock waves from the upper boundary are minimized thanks to a special boundary condition. This has allowed us to increase the duration of the simulations and to make it long enough to perform a statistical analysis of oscillations. The simulations show that deep horizontal motions of the flux tube generate a slow (magnetic) mode and a surface mode. These modes are efficiently transformed into a slow (acoustic) mode in the vA < cS atmosphere. The slow (acoustic) mode propagates vertically along the field lines, forms shocks and remains always within the flux tube. It might deposit effectively the energy of the driver into the chromosphere. When the driver oscillates with a high frequency, above the cut-off, non-linear wave propagation occurs with the same dominant driver period at all heights. At low frequencies, below the cut-off, the dominant period of oscillations changes with height from that of the driver in the photosphere to its first harmonic (half period) in the chromosphere. Depending on the period and on the type of the driver, different shock patterns are observed.Comment: 22 pages 6 color figures, submitted to Solar Physics, proceeding of SOHO 19/ GONG 2007 meeting, Melbourne, Australi