MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

<p>Abstract</p> <p>Background</p> <p>The ability to generate, visualize, and analyze motions of biomolecules has made a significant impact upon modern biology. Molecular Dynamics has gained substantial use, but remains computationally demanding and difficult to setup for many biologists. Elastic network models (ENMs) are an alternative and have been shown to generate the dominant equilibrium motions of biomolecules quickly and efficiently. These dominant motions have been shown to be functionally relevant and also to indicate the likely direction of conformational changes. Most structures have a small number of dominant motions. Comparing computed motions to the structure's conformational ensemble derived from a collection of static structures or frames from an MD trajectory is an important way to understand functional motions as well as evaluate the models. Modes of motion computed from ENMs can be visualized to gain functional and mechanistic understanding and to compute useful quantities such as average positional fluctuations, internal distance changes, collectiveness of motions, and directional correlations within the structure.</p> <p>Results</p> <p>Our new software, MAVEN, aims to bring ENMs and their analysis to a broader audience by integrating methods for their generation and analysis into a user friendly environment that automates many of the steps. Models can be constructed from raw PDB files or density maps, using all available atomic coordinates or by employing various coarse-graining procedures. Visualization can be performed either with our software or exported to molecular viewers. Mixed resolution models allow one to study atomic effects on the system while retaining much of the computational speed of the coarse-grained ENMs. Analysis options are available to further aid the user in understanding the computed motions and their importance for its function.</p> <p>Conclusion</p> <p>MAVEN has been developed to simplify ENM generation, allow for diverse models to be used, and facilitate useful analyses, all on the same platform. This represents an integrated approach that incorporates all four levels of the modeling process - generation, evaluation, analysis, visualization - and also brings to bear multiple ENM types. The intension is to provide a versatile modular suite of programs to a broader audience. MAVEN is available for download at <url>http://maven.sourceforge.net</url>.</p

Color-dependent learning in restrained africanized honey bees

Q2Q1Associative color learning has been demonstrated to be very poor using restrained European honey bees unless the antennae are amputated. Consequently, our understanding of proximate mechanisms in visual information processing is handicapped. Here we test learning performance of Africanized honey bees under restrained conditions with visual and olfactory stimulation using the proboscis extension response (PER) protocol. Restrained individuals were trained to learn an association between a color stimulus and a sugar–water reward. We evaluated performance for ‘absolute’ learning (learned association between a stimulus and a reward) and ‘discriminant’ learning (discrimination between two stimuli). Restrained Africanized honey bees (AHBs) readily learned the association of color stimulus for both blue and green LED stimuli in absolute and discriminatory learning tasks within seven presentations, but not with violet as the rewarded color. Additionally, 24-h memory improved considerably during the discrimination task, compared with absolute association (15–55%). We found that antennal amputation was unnecessary and reduced performance in AHBs. Thus color learning can now be studied using the PER protocol with intact AHBs. This finding opens the way towards investigating visual and multimodal learning with application of neural techniques commonly used in restrained honey bees.https://scienti.minciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000002842Revista Nacional - Indexad

Analyses of the Konus catalogue of gamma-ray bursts with the thermal synchrotron model

Approximately 150 reported gamma bursts of the Konus catalogue using the thermal synchrotron model are analyzed. An overwhelming majority of these spectra can be satsifactorily fitted by theoretical thermal synchrotron spectra of mildly relativistic electrons in strong magnetic fields, making the strong-field neutron star picture at least self-consistent. Valuable additional information is also extracted from various spectral features contained in many of the events

Alcohol: taking a population perspective

Alcohol consumption is a global phenomenon, as is the resultant health, social and economic harm. The nature of these harms varies with different drinking patterns and with the societal and political responses to the burden of harm; nevertheless, alcohol-related chronic diseases have a major effect on health. Strong evidence exists for the effectiveness of different strategies to minimize this damage and those policies that target price, availability and marketing of alcohol come out best, whereas those using education and information are much less effective. However, these policies can be portrayed as anti-libertarian and so viewing them in the context of alcohol-related harm to those other than the drinker, such as the most vulnerable in society, is important. When this strategy is successful, as in Scotland, it has been possible to pass strong and effective legislation, such as for a minimum unit price for alcohol

Imaging and burst location with the EXIST high-energy telescope

The primary instrument of the proposed EXIST mission is a coded mask high energy telescope (the HET), that must have a wide field of view and extremely good sensitivity. It will be crucial to minimize systematic errors so that even for very long total integration times the imaging performance is close to the statistical photon limit. There is also a requirement to be able to reconstruct images on-board in near real time in order to detect and localize gamma-ray bursts. This must be done while the spacecraft is scanning the sky. The scanning provides all-sky coverage and is key to reducing systematic errors. The on-board computational problem is made even more challenging for EXIST by the very large number of detector pixels. Numerous alternative designs for the HET have been evaluated. The baseline concept adopted depends on a unique coded mask with two spatial scales. Monte Carlo simulations and analytic analysis techniques have been used to demonstrate the capabilities of the design and of the proposed two-step burst localization procedure