MQN-Mapplet: Visualization of Chemical Space with Interactive Maps of DrugBank, ChEMBL, PubChem, GDB-11, and GDB-13

The MQN-mapplet is a Java application giving access to the structure of small molecules in large databases via color-coded maps of their chemical space. These maps are projections from a 42-dimensional property space defined by 42 integer value descriptors called molecular quantum numbers (MQN), which count different categories of atoms, bonds, polar groups, and topological features and categorize molecules by size, rigidity, and polarity. Despite its simplicity, MQN-space is relevant to biological activities. The MQN-mapplet allows localization of any molecule on the color-coded images, visualization of the molecules, and identification of analogs as neighbors on the MQN-map or in the original 42-dimensional MQN-space. No query molecule is necessary to start the exploration, which may be particularly attractive for nonchemists. To our knowledge, this type of interactive exploration tool is unprecedented for very large databases such as PubChem and GDB-13 (almost one billion molecules). The application is freely available for download at www.gdb.unibe.ch.

Bifurcation and singularity analysis of a molecular network for the induction of long-term memory.

Withdrawal reflexes of the mollusk Aplysia exhibit sensitization, a simple form of long-term memory (LTM). Sensitization is due, in part, to long-term facilitation (LTF) of sensorimotor neuron synapses. LTF is induced by the modulatory actions of serotonin (5-HT). Pettigrew et al. developed a computational model of the nonlinear intracellular signaling and gene network that underlies the induction of 5-HT-induced LTF. The model simulated empirical observations that repeated applications of 5-HT induce persistent activation of protein kinase A (PKA) and that this persistent activation requires a suprathreshold exposure of 5-HT. This study extends the analysis of the Pettigrew model by applying bifurcation analysis, singularity theory, and numerical simulation. Using singularity theory, classification diagrams of parameter space were constructed, identifying regions with qualitatively different steady-state behaviors. The graphical representation of these regions illustrates the robustness of these regions to changes in model parameters. Because persistent protein kinase A (PKA) activity correlates with Aplysia LTM, the analysis focuses on a positive feedback loop in the model that tends to maintain PKA activity. In this loop, PKA phosphorylates a transcription factor (TF-1), thereby increasing the expression of an ubiquitin hydrolase (Ap-Uch). Ap-Uch then acts to increase PKA activity, closing the loop. This positive feedback loop manifests multiple, coexisting steady states, or multiplicity, which provides a mechanism for a bistable switch in PKA activity. After the removal of 5-HT, the PKA activity either returns to its basal level (reversible switch) or remains at a high level (irreversible switch). Such an irreversible switch might be a mechanism that contributes to the persistence of LTM. The classification diagrams also identify parameters and processes that might be manipulated, perhaps pharmacologically, to enhance the induction of memory. Rational drug design, to affect complex processes such as memory formation, can benefit from this type of analysis.

Capability of a space-based space surveillance system to detect and track objects in GEO, MEO and LEO orbits

In this paper we present the results from the coverage and the orbit determination accuracy simulations performed within the recently completed ESA study “Assessment Study for Space Based Space Surveillance (SBSS) Demonstration System” (Airbus Defence and Space consortium). This study consisted in investigating the capability of a space based optical sensor (SBSS) orbiting in low Earth orbit (LEO) to detect and track objects in GEO (geosynchronous orbit), MEO (medium Earth orbit) and LEO and to determinate and improve initial orbits from such observations. Space based systems may achieve better observation conditions than ground based sensors in terms of astrometric accuracy, detection coverage, and timeliness. The primary observation mode of the proposed SBSS demonstrator is GEO surveillance, i.e. the systematic search and detection of unknown and known objects. GEO orbits are specific and unique orbits from dynamical point of view. A space-based sensor may scan the whole GEO ring within one sidereal day if the orbit and pointing directions are chosen properly. For an efficient survey, our goal was to develop a leak-proof GEO fence strategy. Collaterally, we show that also MEO, LEO and other (GTO,Molniya, etc.) objects would be possible to observe by the system and for a considerable number of LEO objects to down to size of 1 cm we can obtain meaningful statistical data for improvement and validation of space debris environment models

Doppler Orbit Determination of Deep Space Probes by the Bernese GNSS Software: First Results of the Combined Orbit Determination from DSN and Inter-Satellite Ka-Band Data from the Grail Mission

Navigation of deep space probes is most commonly operated using the spacecraft Doppler tracking technique. Orbital parameters are determined from a series of repeated measurements of the frequency shift of a microwave carrier over a given integration time. Currently, both ESA and NASA operate antennas at several sites around the world to ensure the tracking of deep space probes. Just a small number of software packages are nowadays used to process Doppler observations. The Astronomical Institute of the University of Bern (AIUB) has recently started the development of Doppler data processing capabilities within the Bernese GNSS Software. This software has been extensively used for Precise Orbit Determination of Earth orbiting satellites using GPS data collected by on-board receivers and for subsequent determination of the Earth gravity field. In this paper, we present the currently achieved status of the Doppler data modeling and orbit determination capabilities in the Bernese GNSS Software using GRAIL data. In particular we will focus on the implemented orbit determination procedure used for the combined analysis of Doppler and intersatellite Ka-band data. We show that even at this earlier stage of the development we can achieve an accuracy of few mHz on two-way S-band Doppler observation and of 2 µm/s on KBRR data from the GRAIL primary mission phase.

The sensitivity and specificity of a diagnostic test of sequence-space synesthesia

People with sequence-space synesthesia (SSS) report stable visuo-spatial forms corresponding to numbers, days, and months (amongst others). This type of synesthesia has intrigued scientists for over 130 years but the lack of an agreed upon tool for assessing it has held back research on this phenomenon. The present study builds on previous tests by measuring the consistency of spatial locations that is known to discriminate controls from synesthetes. We document, for the first time, the sensitivity and specificity of such a test and suggest a diagnostic cut-off point for discriminating between the groups based on the area bounded by different placement attempts with the same item.

The effect of EU environmental regulation on international trade : restriction of hazardous substance as a trade barrier

In 2003 the Restriction of Hazardous Substances (RoHS) was established in the EU, which limited the trade of machinery, electrical and electronic equipment that have at least one of the substances considered hazardous under RoHS directive. Since countries trading with the EU must comply with this new regulation, it is expected a decrease in value of imports to the EU. In this paper, it is followed the procedures used in Heckman (1979), as well as the extended procedure suggested by Helpman, Melitz, and Rubinstein (2008) to ascertain the effects on the persistence of trade and values of trade.

‘This square is our home!’: the organisation of urban space in the spanish 15M movement

Why should a progressive planner/urbanist pay attention to the Spanish 15M movement? From a disciplinary standpoint, its most complex and interesting aspect, which could hypothetically be transferred to other contexts (as in fact happened in the Occupy Wall Street and Occupy London movements), is its 'spatiality'. This article analyses the spatial practices of the so called #spanishrevolution, one of the 2011 social movements that showed the possibility for a new collective appropriation and self-management (autogestion) of urban public space. Although the political goals of the movement were vague at the time of its inception, the practices and spatial imaginaries deployed by it have become consolidated and proven to be yet another of its more successful facets in promoting the spreading and organisation of the protest, making it a phenomenon that calls for reflection on the part of urban thinkers and planners.

Physics and applications of electrodynamic space tethers

Basic effects and dynamical and electrical contact issues in the physics of (electrodynamic space) bare tethers are discussed. Scientific experiments and powerpropulsion applications, including a paradoxical use of bare tethers in outer-planet exploration,are considered.

New York: the revitalization of public space. Recent interventions in the Manhattan grid

La reticula de Nueva York ha sido un formato de nuevos planteamientos de "hacer ciudad" desde hace dos siglos. Esta ultima decada ha suspuesto un periodo fructifero para el espacio publico neoyorkino bajo la administracion de Michael Bloomerg. Esta revitalizacion no habria podido ser posible sin la reactivacion de factores de espacio publico que ya existian: la reticula, la legislacion publica y el rol del ciudadano. El ciudadano juega un papel fundamental en la ciudad, ya que es usuario, critico y promotor de espacio publico. Sin embargo, en ocasiones no es evidente para quien o quienes estan pensados los nuevos espacios publicos en la ciudad. Desde esta perspectiva, podemos identificar diferentes usuarios en la ciudad y analizar formulas recientes de espacio publico para cada uno de ellos: el vecino, el ciudadano, y el visitante. En palabras de Jane Jacobs: " las ciudades tienen la capacidad de proveer algo para todo el mundo, solo porque, y solo cuando, han sido proyectadas por todo el mundo".

Fractal parameters of pore space from CT images of soils under contrasting management practices

Soil structure plays an important role in flow and transport phenomena, and a quantitative characterization of the spatial heterogeneity of the pore space geometry is beneficial for prediction of soil physical properties. Morphological features such as pore-size distribution, pore space volume or pore?solid surface can be altered by different soil management practices. Irregularity of these features and their changes can be described using fractal geometry. In this study, we focus primarily on the characterization of soil pore space as a 3D geometrical shape by fractal analysis and on the ability of fractal dimensions to differentiate between two a priori different soil structures. We analyze X-ray computed tomography (CT) images of soils samples from two nearby areas with contrasting management practices. Within these two different soil systems, samples were collected from three depths. Fractal dimensions of the pore-size distributions were different depending on soil use and averaged values also differed at each depth. Fractal dimensions of the volume and surface of the pore space were lower in the tilled soil than in the natural soil but their standard deviations were higher in the former as compared to the latter. Also, it was observed that soil use was a factor that had a statistically significant effect on fractal parameters. Fractal parameters provide useful complementary information about changes in soil structure due to changes in soil management. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0218348X14400118?queryID=%24%7BresultBean.queryID%7D&

El comportamiento del viento en la morfología urbana y su incidencia en el uso estancial del espacio público, Punta Arenas, Chile = The behavior of wind in urban morphology and its incidence in the resting use of public space, Punta Arenas, Chile

El comportamiento del viento en la morfología urbana y su incidencia en el uso estancial del espacio público, Punta Arenas, Chile = The behavior of wind in urban morphology and its incidence in the resting use of public space, Punta Arenas, Chile