Visualizing 2D Flows with Animated Arrow Plots

Flow fields are often represented by a set of static arrows to illustrate scientific vulgarization, documentary film, meteorology, etc. This simple schematic representation lets an observer intuitively interpret the main properties of a flow: its orientation and velocity magnitude. We propose to generate dynamic versions of such representations for 2D unsteady flow fields. Our algorithm smoothly animates arrows along the flow while controlling their density in the domain over time. Several strategies have been combined to lower the unavoidable popping artifacts arising when arrows appear and disappear and to achieve visually pleasing animations. Disturbing arrow rotations in low velocity regions are also handled by continuously morphing arrow glyphs to semi-transparent discs. To substantiate our method, we provide results for synthetic and real velocity field datasets

The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive

BACKGROUND The Medicago truncatula 2HA seed line is highly embryogenic while the parental line Jemalong rarely produces embryos. The 2HA line was developed from one of the rare Jemalong regenerates and this method for obtaining a highly regenerable genotype in M. truncatula is readily reproducible suggesting an epigenetic mechanism. Microarray transcriptomic analysis showed down regulation of an ETHYLENE INSENSITIVE 3-like gene in 2HA callus which provided an approach to investigating epigenetic regulation of genes related to ethylene signalling and the 2HA phenotype. Ethylene is involved in many developmental processes including somatic embryogenesis (SE) and is associated with stress responses. RESULTS Microarray transcriptomic analysis showed a significant number of up-regulated transcripts in 2HA tissue culture, including nodule and embryo specific genes and transposon-like genes, while only a few genes were down-regulated, including an EIN3-like gene we called MtEIL1. This reduced expression was associated with ethylene insensitivity of 2HA plants that was further investigated. The weak ethylene insensitivity affected root and nodule development. Sequencing of MtEIL1 found no difference between 2HA and wild-type plants. DNA methylation analysis of MtEIL1 revealed significant difference between 2HA and wild-type plants. Tiling arrays demonstrated an elevated level of miRNA in 2HA plants that hybridised to the antisense strand of the MtEIL1 gene. AFLP-like methylation profiling revealed more differences in DNA methylation between 2HA and wild-type. Segregation analysis demonstrated the recessive nature of the eil1 phenotype and the dominant nature of the SE trait. CONCLUSIONS We have demonstrated that EIL1 of Medicago truncatula (MtEIL1) is epigenetically silenced in the 2HA seed line. The possible cause is an elevated level of miRNA that targets its 3'UTR and is also associated with DNA methylation of MtEIL1. Down regulation of MtEIL1 makes it possible to form nodules in the presence of ethylene and affects root growth under normal conditions. Segregation analysis showed no association between MtEIL1 expression and SE in culture but the role and mechanism of ethylene signalling in the process of plant regeneration through SE requires further investigation. The work also suggests that epigenetic changes to a particular gene induced in culture can be fixed in regenerated plants.This work was funded by the Australian Research Council (CEO348212) through the ARC Centre of Excellence for Integrative Legume Research (CILR)

SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

Summary: SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios. The spatially explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources. A coalescent-based approach is used to generate genetic markers mostly used in population genetics studies (DNA sequences, SNPs, STRs or RFLPs). Various combinations of independent, fully or partially linked genetic markers can be produced under a recombination model based on the ancestral recombination graph. Competition between two populations (or species) can also be simulated with user-defined levels of admixture between the two populations. SPLATCHE2 may be used to generate the expected genetic diversity under complex demographic scenarios and can thus serve to test null hypotheses. For model parameter estimation, SPLATCHE2 can easily be integrated into an Approximate Bayesian Computation (ABC) framework. Availability and implementation: SPLATCHE2 is a C++ program compiled for Windows and Linux platforms. It is freely available at www.splatche.com, together with its related documentation and example data. Contact: [email protected]

Genetic isolation by distance and landscape connectivity in the American marten ( Martes americana )

Empirical studies of landscape connectivity are limited by the difficulty of directly measuring animal movement. ‘Indirect' approaches involving genetic analyses provide a complementary tool to ‘direct' methods such as capture-recapture or radio-tracking. Here the effect of landscape on dispersal was investigated in a forest-dwelling species, the American marten (Martes americana) using the genetic model of isolation by distance (IBD). This model assumes isotropic dispersal in a homogeneous environment and is characterized by increasing genetic differentiation among individuals separated by increasing geographic distances. The effect of landscape features on this genetic pattern was used to test for a departure from spatially homogeneous dispersal. This study was conducted on two populations in homogeneous vs. heterogeneous habitat in a harvested boreal forest in Ontario (Canada). A pattern of IBD was evidenced in the homogeneous landscape whereas no such pattern was found in the near-by harvested forest. To test whether landscape structure may be accountable for this difference, we used effective distances that take into account the effect of landscape features on marten movement instead of Euclidean distances in the model of isolation by distance. Effective distances computed using least-cost modeling were better correlated to genetic distances in both landscapes, thereby showing that the interaction between landscape features and dispersal in Martes americana may be detected through individual-based analyses of spatial genetic structure. However, the simplifying assumptions of genetic models and the low proportions in genetic differentiation explained by these models may limit their utility in quantifying the effect of landscape structur

AccessMod 3.0: computing geographic coverage and accessibility to health care services using anisotropic movement of patients

<p>Abstract</p> <p>Background</p> <p>Access to health care can be described along four dimensions: geographic accessibility, availability, financial accessibility and acceptability. Geographic accessibility measures how physically accessible resources are for the population, while availability reflects what resources are available and in what amount. Combining these two types of measure into a single index provides a measure of geographic (or spatial) coverage, which is an important measure for assessing the degree of accessibility of a health care network.</p> <p>Results</p> <p>This paper describes the latest version of AccessMod, an extension to the Geographical Information System ArcView 3.×, and provides an example of application of this tool. AccessMod 3 allows one to compute geographic coverage to health care using terrain information and population distribution. Four major types of analysis are available in AccessMod: (1) modeling the coverage of catchment areas linked to an existing health facility network based on travel time, to provide a measure of physical accessibility to health care; (2) modeling geographic coverage according to the availability of services; (3) projecting the coverage of a scaling-up of an existing network; (4) providing information for cost effectiveness analysis when little information about the existing network is available. In addition to integrating travelling time, population distribution and the population coverage capacity specific to each health facility in the network, AccessMod can incorporate the influence of landscape components (e.g. topography, river and road networks, vegetation) that impact travelling time to and from facilities. Topographical constraints can be taken into account through an anisotropic analysis that considers the direction of movement. We provide an example of the application of AccessMod in the southern part of Malawi that shows the influences of the landscape constraints and of the modes of transportation on geographic coverage.</p> <p>Conclusion</p> <p>By incorporating the demand (population) and the supply (capacities of heath care centers), AccessMod provides a unifying tool to efficiently assess the geographic coverage of a network of health care facilities. This tool should be of particular interest to developing countries that have a relatively good geographic information on population distribution, terrain, and health facility locations.</p

POTs: Protective Optimization Technologies

Algorithmic fairness aims to address the economic, moral, social, and political impact that digital systems have on populations through solutions that can be applied by service providers. Fairness frameworks do so, in part, by mapping these problems to a narrow definition and assuming the service providers can be trusted to deploy countermeasures. Not surprisingly, these decisions limit fairness frameworks' ability to capture a variety of harms caused by systems. We characterize fairness limitations using concepts from requirements engineering and from social sciences. We show that the focus on algorithms' inputs and outputs misses harms that arise from systems interacting with the world; that the focus on bias and discrimination omits broader harms on populations and their environments; and that relying on service providers excludes scenarios where they are not cooperative or intentionally adversarial. We propose Protective Optimization Technologies (POTs). POTs provide means for affected parties to address the negative impacts of systems in the environment, expanding avenues for political contestation. POTs intervene from outside the system, do not require service providers to cooperate, and can serve to correct, shift, or expose harms that systems impose on populations and their environments. We illustrate the potential and limitations of POTs in two case studies: countering road congestion caused by traffic-beating applications, and recalibrating credit scoring for loan applicants.Comment: Appears in Conference on Fairness, Accountability, and Transparency (FAT* 2020). Bogdan Kulynych and Rebekah Overdorf contributed equally to this work. Version v1/v2 by Seda G\"urses, Rebekah Overdorf, and Ero Balsa was presented at HotPETS 2018 and at PiMLAI 201