Criticality of the "critical state" of granular media: Dilatancy angle in the tetris model

The dilatancy angle describes the propensity of a granular medium to dilate under an applied shear. Using a simple spin model (the ``tetris'' model) which accounts for geometrical ``frustration'' effects, we study such a dilatancy angle as a function of density. An exact mapping can be drawn with a directed percolation process which proves that there exists a critical density $\rho_c$ above which the system expands and below which it contracts under shear. When applied to packings constructed by a random deposition under gravity, the dilatancy angle is shown to be strongly anisotropic, and it constitutes an efficient tool to characterize the texture of the medium.Comment: 7 pages RevTex, 8eps figure, to appear in Phys. Rev.

Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species

Internal avalanches in models of granular media

We study the phenomenon of internal avalanching within the context of recently introduced lattice models of granular media. The avalanche is produced by pulling out a grain at the base of the packing and studying how many grains have to rearrange before the packing is once more stable. We find that the avalanches are long-ranged, decaying as a power-law. We study the distriution of avalanches as a function of the density of the packing and find that the avalanche distribution is a very sensitive structural probe of the system.Comment: 12 pages including 9 eps figures, LaTeX. To appear in Fractal

A community annotation system for Musa genomes

Poster presented at ISHS/ProMusa Banana Symposium Global Perspectives on Asian Challenges. Guangzhou (China), 14-18 Sep 200

Loneliness, Depression, and Inflammation: Evidence from the Multi-Ethnic Study of Atherosclerosis

Objective Both objective and subjective aspects of social isolation have been associated with alterations in immune markers relevant to multiple chronic diseases among older adults. However, these associations may be confounded by health status, and it is unclear whether these social factors are associated with immune functioning among relatively healthy adults. The goal of this study was to examine the associations between perceived loneliness and circulating levels of inflammatory markers among a diverse sample of adults. Methods Data come from a subset of the Multi-Ethnic Study of Atherosclerosis (n = 441). Loneliness was measured by three items derived from the UCLA Loneliness Scale. The association between loneliness and C-reactive protein (CRP) and fibrinogen was assessed using multivariable linear regression analyses. Models were adjusted for demographic and health characteristics. Results Approximately 50% of participants reported that they hardly ever felt lonely and 17.2% felt highly lonely. Individuals who were unmarried/unpartnered or with higher depressive symptoms were more likely to report being highly lonely. There was no relationship between perceived loneliness and ln(CRP) (β = -0.051, p = 0.239) adjusting for demographic and health characteristics. Loneliness was inversely associated with ln(fibrinogen) (β = -0.091, p = 0.040), although the absolute magnitude of this relationship was small. Conclusion These results indicate that loneliness is not positively associated with fibrinogen or CRP among relatively healthy middle-aged adults

Crop ontology in support of conservation and use of banana genetic resources

Poster presented at Workshop on Crop Ontology and Phenotyping Data Interoperability. Montpellier (France), 31 Mar-4 Apr 201

Using an agent-based model to simulate children’s active travel to school

Abstract Background Despite the multiple advantages of active travel to school, only a small percentage of US children and adolescents walk or bicycle to school. Intervention studies are in a relatively early stage and evidence of their effectiveness over long periods is limited. The purpose of this study was to illustrate the utility of agent-based models in exploring how various policies may influence children’s active travel to school. Methods An agent-based model was developed to simulate children’s school travel behavior within a hypothetical city. The model was used to explore the plausible implications of policies targeting two established barriers to active school travel: long distance to school and traffic safety. The percent of children who walk to school was compared for various scenarios. Results To maximize the percent of children who walk to school the school locations should be evenly distributed over space and children should be assigned to the closest school. In the case of interventions to improve traffic safety, targeting a smaller area around the school with greater intensity may be more effective than targeting a larger area with less intensity. Conclusions Despite the challenges they present, agent based models are a useful complement to other analytical strategies in studying the plausible impact of various policies on active travel to school.http://deepblue.lib.umich.edu/bitstream/2027.42/112566/1/12966_2012_Article_757.pd

Shear band dynamics from a mesoscopic modeling of plasticity

The ubiquitous appearance of regions of localized deformation (shear bands) in different kinds of disordered materials under shear is studied in the context of a mesoscopic model of plasticity. The model may or may not include relaxational (aging) effects. In the absence of relaxational effects the model displays a monotonously increasing dependence of stress on strain-rate, and stationary shear bands do not occur. However, in start up experiments transient (although long lived) shear bands occur, that widen without bound in time. I investigate this transient effect in detail, reproducing and explaining a t^1/2 law for the thickness increase of the shear band that has been obtained in atomistic numerical simulations. Relaxation produces a negative sloped region in the stress vs. strain-rate curve that stabilizes the formation of shear bands of a well defined width, which is a function of strain-rate. Simulations at very low strain-rates reveal a non-trivial stick-slip dynamics of very thin shear bands that has relevance in the study of seismic phenomena. In addition, other non-stationary processes, such as stop-and-go, or strain-rate inversion situations display a phenomenology that matches very well the results of recent experimental studies.Comment: 10 pages, 10 figure

Stability of Plane-Parallel Vibrational Flow In a Two-Layer System

The stability of the interface separating two immiscible incompressible fluids of different densities and viscosities is considered in the case of fluids filling a cavity which performs horizontal harmonic oscillation. There exists a simple basic state which corresponds to the unperturbed interface and plane-parallel unsteady counter flows; the properties of this state are examined. A linear stability problem for the interface is formulated and solved a) for both inviscid and b) for both viscous fluids. A transformation is found which reduces the linear stability problem under inviscid approximation to the Mathieu equation. The parametric resonant regions of instability associated with the intensification of capillary-gravity waves at the interface are examined and the results are compared to those found in the viscous case in a fully numerical investigation.Comment: 15 pages, 6 figures; soon to appear in European Journal of Fluid Mechanic

Inorganic Chemistry in the Mountain Critical Zone : Are the mountain water towers of contemporary society under threat by trace contaminants ?

Potentially harmful trace elements (PHTEs) do not accumulate homogeneously over mountainous area. Generally, highland areas receive more wet deposition, aerosols, and ions than surrounding lowlands ones, mainly due to orographic enhancement. Within mountainous areas, however, the accumulation of PHTEs is much more complex. Direct cloud deposition of contaminants could act as an important pathway of deposition either from a regional low-altitude, cloud level, orographic clouds, or haze whose frequency of occurrence is much higher than surrounding lowlands areas. The accumulation legacy of PHTEs from local human activities should also be considered when investigating PHTE distribution in mountainous areas. Combined with other phenomena, the PHTE accumulation patterns could be highly variable depending on local topography, dominant winds, and vegetation cover, as well as present and past local practices. Despite their remoteness, mountain ecosystems are highly sensitive to PHTEs loadings