Permutation-invariant distance between atomic configurations

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e. fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the Root Mean Square Distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e. their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity

Blockade of adenosine A2A receptors prevents protein phosphorylation in the striatum induced by cortical stimulation

©2006 Society for NeurosciencePrevious studies have shown that cortical stimulation selectively activates extracellular signal-regulated kinase 1/2 (ERK1/2) phosphorylation and immediate early gene expression in striatal GABAergic enkephalinergic neurons. In the present study, we demonstrate that blockade of adenosine A2A receptors with caffeine or a selective A2A receptor antagonist counteracts the striatal activation of cAMP– protein kinase A cascade (phosphorylation of the Ser845 residue of the glutamate receptor 1 subunit of the AMPA receptor) and mitogenactivated protein kinase (ERK1/2 phosphorylation) induced by the in vivo stimulation of corticostriatal afferents. The results indicate that A2A receptors strongly modulate the efficacy of glutamatergic synapses on striatal enkephalinergic neurons.This work was supported by the Intramural Research Program of the National Institutes of Health, National Institute on Drug Abuse, Department of Health and Human Services

Magma flow inferred from AMS fabrics in a layered mafic sill, Insizwa, South Africa

The Insizwa sill, is a 25-km-diameter, >1000-m-thick layered mafic intrusion, part of the Karoo Igneous Province in South Africa. The peridotitic and gabbronoritic rocks are undeformed and mineral fabrics demonstrably result from magma flow. A horizontal, centimeter-scale model layering is visible in numerous outcrops. Plagioclase crystals are both tabular and elongated. Their preferred orientation, parallel to the layering, forms a foliation and a NW–SE lineation, respectively interpreted as the magma flow plane and flow direction. Throughout the 78 stations of this study (699 specimens), magnetic susceptibilities (K[subscript m]) range from 750 to 10,000×10[superscript (−6)] SI. The magnetic anisotropy (P[subscript j]) ranges from 1.03 to 1.08. Magnetic ellipsoids are both prolate and oblate (average T[subscript j]≈0). Anisotropy of magnetic susceptibility (AMS) fabrics are dominated by multidomain to pseudo-single domain magnetite. High-field magnetic experiments indicate that the paramagnetic contribution from the mafic silicates is less than 50 percentage for low susceptibility rock types. The anisotropy results from magnetite grain shape solely as shown by no significant increase in P[subscript j] with increasing K[subscript m]. The magnetic lineation (305°, 05°) is consistent throughout the sill at various scales and coincides with the mineral lineation in average. In contrast, the magnetic foliation (125° NE 10°) is generally perpendicular to the mineral foliation and to the layering. Several explanations for this odd configuration are discussed. The variations of magnetic parameters across the layering and field observations point to a multiple injection. The magnetic lineation is consistent with the presence of a single feeder dike situated to the SE of the sill

Impact of 40 years poplar cultivation on soil carbon stocks and greenhouse gas fluxes

International audienceWithin the JRC Kyoto Experiment in the Regional Park and UN-Biosphere Reserve "Parco Ticino" (North-Italy, near Pavia), the soil carbon stocks and fluxes of CO2, N2O, and CH4 were measured in a poplar plantation in comparison with a natural mesohygrophilous deciduous forest nearby, which represents the pristine land cover of the area. Soil fluxes were measured using the static and dynamic closed chamber techniques for CH4 N2O, and CO2, respectively. We made further a pedological study to relate the spatial variability found with soil parameters. Annual emission fluxes of N2O and CO2 and deposition fluxes of CH4 were calculated for the year 2003 for the poplar plantation and compared to those measured at the natural forest site. N2O emissions at the poplar plantation were 0.15$plusmn;0.1 g N2O m-2 y-1 and the difference to the emissions at the natural forest of 0.07±0.06 g N2O m-2 y-1 are partly due to a period of high emissions after the flooding of the site at the end of 2002. CH4 consumption at the natural forest was twice as large as at the poplar plantation. In comparison to the relict forest, carbon stocks in the soil under the poplar plantation were depleted by 61% of surface (10 cm) carbon and by 25% down the profile under tillage (45 cm). Soil respiration rates were not significant different at both sites with 1608±1053 and 2200±791 g CO2 m-2 y-1 at the poplar plantation and natural forest, respectively, indicating that soil organic carbon is much more stable in the natural forest. In terms of the greenhouse gas budget, the non-CO2 gases contributed minor to the overall soil balance with only 0.9% (N2O) and -0.3% (CH4 of CO2-eq emissions in the natural forest, and 2.7% (N2O) and -0.2% of CO2-eq. emissions in the poplar plantation. The very high spatial variability of soil fluxes within the two sites was related to the morphology of the floodplain area, which was formed by the historic course of the Ticino river and led to a small-scale (tenth of meters) variability in soil texture and to small-scale differences in elevation. Differences of site conditions are reflected by differences of inundation patterns, ecosystem productivity, CO2 and N2O emission rates, and soil contents of carbon and nitrogen. Additional variability was observed during a flooding event and after fertilisation at the poplar site. Despite of this variability, the two sites are comparable as both originate from alluvial deposits. The study shows that changes in soil carbon stocks and related fertility are the most visible phenomena after 40 years of land use change from a pristine forest to a fast growing poplar plantation. Therefore, the conservation and careful management of existing carbon stocks deserves highest priority in the context of the Kyoto Protocol

A model ensemble generator to explore structural uncertainty in karst systems with unmapped conduits

Karst aquifers are characterized by high-conductivity conduits embedded in a low-conductivity fractured matrix, resulting in extreme heterogeneity and variable groundwater flow behavior. The conduit network controls groundwater flow, but is often unmapped, making it difficult to apply numerical models to predict system behavior. This paper presents a multi-model ensemble method to represent structural and conceptual uncertainty inherent in simulation of systems with limited spatial information, and to guide data collection. The study tests the new method by applying it to a well-mapped, geologically complex long-term study site: the Gottesacker alpine karst system (Austria/Germany). The ensemble generation process, linking existing tools, consists of three steps: creating 3D geologic models using GemPy (a Python package), generating multiple conduit networks constrained by the geology using the Stochastic Karst Simulator (a MATLAB script), and, finally, running multiple flow simulations through each network using the Storm Water Management Model (C-based software) to reject nonbehavioral models based on the fit of the simulated spring discharge to the observed discharge. This approach captures a diversity of plausible system configurations and behaviors using minimal initial data. The ensemble can then be used to explore the importance of hydraulic flow parameters, and to guide additional data collection. For the ensemble generated in this study, the network structure was more determinant of flow behavior than the hydraulic parameters, but multiple different structures yielded similar fits to the observed flow behavior. This suggests that while modeling multiple network structures is important, additional types of data are needed to discriminate between networks

The stochastic simulation of karst conduit network structure using anisotropic fast marching, and its application to a geologically complex alpine karst system

Anisotropic fast-marching algorithms are computationally efficient tools for generating realistic maps of karst conduit networks, constrained by both the spatial extent and the orientation of karstifiable geologic units. Existing models to generate conduit network maps are limited either by high computational requirements (for chemistry-based models) or by their inability to incorporate the effects of elevation and orientation gradients (for isotropic fast-marching models). The new anisotropic fast-marching approach described here provides a significant improvement, though it imitates rather than reproduces actual speleogenetic processes. It can rapidly generate a stochastic ensemble of plausible networks from basic geologic information, which can also be used as input to karst-appropriate flow models. This paper introduces an open-source, easy-to-use implementation through the Python package pyKasso, then describes its application to a well-mapped geologically complex long-term study site: the Gottesacker alpine karst system (Germany/Austria). Groundwater flow in this system is exceptionally well understood from speleological investigations and tracer tests. Conduit formation primarily occurs at the base of the karst aquifer, following plunging synclines. Although previous attempts to reproduce the conduit network at this site yielded implausible network maps, pyKasso quickly generated networks faithful to the known conduit system. However, the model was only able to generate these realistic networks when the inlet-outlet connections of the system were correctly assigned, highlighting the importance of pairing modeling efforts with field tracer tests. Therefore, a model ensemble method is also presented, to optimize field efforts by identifying the most informative tracer tests to perform

Deformation and magnetic fabrics in ductile shear zones: A review

The Anisotropy of Magnetic Susceptibility (AMS) is a well-established petrofabric tool for indicating relative strain and microstructural character and has been validated on various rock types and different structural settings. The magnetic susceptibility of a rock (K) depends primarily on the nature and abundance of magnetic minerals. The physical arrangement and lattice-preferred orientation of these magnetic minerals give rise to magnetic anisotropy. The AMS scalar parameters most commonly used to constrain strain include the corrected degree of anisotropy (P'> 1), a proxy for fabric intensity, and the shape factor (- 1 ≤ T≤ + 1), an indicator of the magnetic fabric symmetry (prolate vs. oblate).A number of studies have shown that a positive correlation generally exists between P' and strain. Thus, the AMS shows a great potential as a tool for examining deformation in geologic structures characterized by large strain gradients such as shear zones. However, a number of caveats exist: (i) The increase of P' with strain cannot be solely attributed to deformation because P' also increases with K regardless of deformation; (ii) Strain across shear zones is typically heterogeneous and is often localized in units of different lithology, thus making the separation of the lithological and strain controls on AMS difficult; also, deformation is commonly accompanied by mineral segregation or fluid-rock interaction that induces changes in magnetic mineralogy; (iii) Even if the undeformed lithology was uniform across a shear zone, variations in strain rate or temperature may result in different deformation mechanisms; hence, the relationship between P' and strain depends strongly on both the mineral carriers of AMS and on deformation mechanisms; and (iv) The AMS is unable to resolve composite fabrics, such as those resulting from S-C structures, where minerals on the C and S planes, respectively, contribute to AMS

Are zona pellucida genes involved in recurrent oocyte lysis observed during in vitro fertilization?

PURPOSE: Complete oocyte lysis in in vitro fertilization (IVF) is a rare event, but one against which we remain helpless. The recurrence of this phenomenon in some women in each of their IVF attempts, regardless of treatment, together with the results of animal experiments led us to investigate the possible involvement of the genes encoding for the glycoproteins constituting the zona pellucida (ZP). PATIENTS & METHODS: Over the last ten years, during which we treated over 500 women each year, three women suffered recurrent oocyte lysis during their IVF attempts in our Centre for Reproductive Biology. For each of these three cases, we sequenced the four genes and promoter sequences encoding the glycoproteins of the ZP. The sequence variations likely to cause a change in protein expression or structure, were investigated in a control group of 35 women who underwent IVF without oocyte lysis and with normal rates of fertilization. RESULTS & CONCLUSION: We found no mutations in the ZP genes sequenced. Only some polymorphisms present in the control group and in the general population were detected, excluding their specific involvement in the phenotype observed. Thus, although we suspected that complete oocyte lysis was due to a genetic cause, it did not seem possible to directly incriminate the genes encoding the proteins of the ZP in the observed phenotype. Further study of the genes involved in the processing and organization of ZP glycoproteins may allow elucidation of the mechanism underlying recurrent oocyte lysis during in vitro fertilization