Visualization of Barrier Tree Sequences Revisited

The increasing complexity of models for prediction of the native spatial structure of RNA molecules requires visualization methods that help to analyze and understand the models and their predictions. This paper improves the visualization method for sequences of barrier trees previously published by the authors. The barrier trees of these sequences are rough topological simplifications of changing folding landscapes – energy landscapes in which kinetic folding takes place. The folding landscapes themselves are generated for RNA molecules where the number of nucleotides increases. Successive landscapes are thus correlated and so are the corresponding barrier trees. The landscape sequence is visualized by an animation of a barrier tree that changes with time. The animation is created by an adaption of the foresight layout with tolerance algorithm for dynamic graph layout problems. Since it is very general, the main ideas for the adaption are presented: construction and layout of a supergraph, and how to build the final animation from its layout. Our previous suggestions for heuristics lead to visually unpleasing results for some datasets and, generally, suffered from a poor usage of available screen space. We will present some new heuristics that improve the readability of the final animation

Tree species’ tolerance to water stress, salinity and fire

According to climate change predictions, water availability might change dramatically in Europe and adjacent regions. This change will undoubtedly have an adverse effect on existing tree species and affect their ability to cope with a lack or an excess of water, changes in annual precipitation patterns, soil salinity and fire disturbance. The following chapter will describe tree species and proven-ances used in European forestry practice which are the most suitable to deal with water stress, salinity and fire. Each subchapter starts with a brief description of each of the stress factors and discusses the predictions of the likelihood of their occurrence in the near future according to the climate change scenarios. Tree spe-cies and their genotypes able to cope with particular stress factor, together with indication of their use by forest managers are then introduced in greater detail

Birds as Ecological Indicators at the University of Pennsylvania

Birds are ubiquitous, intricately connected to habitat, sensitive to environmental changes and their presence can indicate ecosystem function. Situated along a major bird migration route, the University of Pennsylvania (Penn) provides important stop-over habitat for migrating birds and foraging and nesting habitat for resident birds. Analysis of diversity, abundance and behavior reveals how the campus landscape provides essential habitat. Point-count surveys and area searches at representative habitat typologies on campus were conducted during migration and breeding seasons in 2018 and 2019. Systematic and incidental data collection resulted in 84 species from 34 families, with a total of 3,777 detections of birds recorded. As Penn’s Landscape Planner, I play a pivotal role in furthering the university’s sustainability goals and influencing landscape design and management on campus. This research establishes quantitative data that can define best practices and inform future landscape standards. Enhancing bird-friendly design guidelines and improving campus habitat and management strategies could have a broad impact on landscape connectivity and bird species richness. Future monitoring studies are recommended in order to quantify trends linking campus environmental health with bird species richness

Contours in Visualization

This thesis studies the visualization of set collections either via or defines as the relations among contours. In the first part, dynamic Euler diagrams are used to communicate and improve semimanually the result of clustering methods which allow clusters to overlap arbitrarily. The contours of the Euler diagram are rendered as implicit surfaces called blobs in computer graphics. The interaction metaphor is the moving of items into or out of these blobs. The utility of the method is demonstrated on data arising from the analysis of gene expressions. The method works well for small datasets of up to one hundred items and few clusters. In the second part, these limitations are mitigated employing a GPU-based rendering of Euler diagrams and mixing textures and colors to resolve overlapping regions better. The GPU-based approach subdivides the screen into triangles on which it performs a contour interpolation, i.e. a fragment shader determines for each pixel which zones of an Euler diagram it belongs to. The rendering speed is thus increased to allow multiple hundred items. The method is applied to an example comparing different document clustering results. The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Adapting popular graph drawing approaches to the problem of contour tree drawing it is found that they are unable to convey this information. Five aesthetic criteria for drawing contour trees are proposed and a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria is presented. The implementation is fast and effective for contour tree sizes usually used in interactive systems and also produces readable pictures for larger trees. Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods to analyze these model\''s validity. The fourth part of the thesis focuses on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; they are huge and high dimensional. Their most salient features are described by their so-called barrier tree -- a contour tree for discrete observation spaces. The changing folding landscapes of a growing RNA chain are visualized as an animation of the corresponding barrier tree sequence. The animation is created as an adaption of the foresight layout with tolerance algorithm for dynamic graph layout. The adaptation requires changes to the concept of supergraph and it layout. The thesis finishes with some thoughts on how these approaches can be combined and how the task the application should support can help inform the choice of visualization modality

Visualization of Barrier Tree Sequences

Dynamical models that explain the formation of spatial structures of RNA molecules have reached a complexity that requires novel visualization methods that help to analyze the validity of these models. We focus on the visualization of so-called folding landscapes of a growing RNA molecule. Folding landscapes describe the energy of a molecule as a function of its spatial configuration; thus they are huge and high dimensional. Their most salient features, however, are encapsulated by their so-called barrier tree that reflects the local minima and their connecting saddle points. For each length of the growing RNA chain there exists a folding landscape. We visualize the sequence of folding landscapes by an animation of the corresponding barrier trees. To generate the animation, we adapt the foresight layout with tolerance algorithm for general dynamic graph layout problems. Since it is very general, we give a detailed description of each phase: constructing a supergraph for the trees, layout of that supergraph using a modified DOT algorithm, and presentation techniques for the final animatio

Cell wall functional activity and metal accumulation of halophytic plant species Plantago maritima and Triglochin maritima on the White Sea littoral zone (NW Russia)

The presented study supplements the knowledge on ion-exchange capacity, swelling capacity (elasticity) of the plant cell wall, and the accumulation of heavy metals in halophytic species Plantago maritima and Triglochin maritima in the tidal zone of the White Sea western coast. The littoral soils of the coastal territories are sandy or rocky-sandy, medium and slightly saline with poor content of organic substances, Mn, Zn, Ni, and Pb. Studied soils are considered as uncontaminated by heavy metals because they contain background amounts of Fe and Cu. Sea water is significantly polluted by Fe (3.8 MPC) and Ni (55 MPC), has poor content of Zn and Cu and background level of Pb and Mn. The coastal dominant plant species P. maritima and T. maritima were characterized by intensive metals accumulation which was reflected in the coefficient of biological absorption (CBA) of metal by a whole plant. For P. maritima the following metal accumulation series was obtained: Cu (3.29)> Zn (2.81)> Ni (1.57)> Pb (1.30)> Mn (1.21)> Fe (0.97), and for T. maritima: Ni (3.80)> Fe (2.08)> Cu (1.91)> Zn (1.84)> Pb (1.51)> Mn (1.31). Roots accumulated 50–70% of Ni, Cu, Zn, Pb and Mn of the total metal content in the plant while leaves and stems contained 30–50%. Fe was allocated mainly in the roots (80%). The ion-exchange capacity of the plant cell wall for P. maritima and T. maritima was established as follows correspondingly: 3570–3700 and 2710–3070 μmol g-1 dry cell weight per leaf; 2310–2350 and 1160–1250 μmol g-1 dry cell weight per root

Modeling Heat Exchange of White-Tailed Deer (Odocoileus Virginianus) In the Built and Natural Environments of Fire Island, New York

The potential consequences of climate warming on the behavior and distribution of endotherms pose management challenges. This is especially true for organisms that are able to exploit both natural and anthropogenic environments, such as the white-tailed deer. I developed a biophysical model of operative temperature based on various forms of heat transfer between deer and their environment on Fire Island National Seashore using measured variables collected from a small micrometeorological sensor network. I compared operative temperature to observed values of Vernon globe temperature in order to validate the use of the globe as a representation of heat exchange for deer. The globe was an adequate proxy, with minimal difference between the predicted and observed values and compatibility in patterns over the diel. Identifying critical thermal thresholds for deer in a changing landscape will be necessary in order to understand and address future human-wildlife interactions

Rodent Biology and Management; Abstracts of papers presented at the International Conference on Rodent Biology and Management, held at Beijing, China, 5-9 October 1998

Farm Management,