Relating cell shape and mechanical stress in a spatially disordered epithelium using a vertex-based model

Using a popular vertex-based model to describe a spatially disordered planar epithelial monolayer, we examine the relationship between cell shape and mechanical stress at the cell and tissue level. Deriving expressions for stress tensors starting from an energetic formulation of the model, we show that the principal axes of stress for an individual cell align with the principal axes of shape, and we determine the bulk effective tissue pressure when the monolayer is isotropic at the tissue level. Using simulations for a monolayer that is not under peripheral stress, we fit parameters of the model to experimental data for Xenopus embryonic tissue. The model predicts that mechanical interactions can generate mesoscopic patterns within the monolayer that exhibit long-range correlations in cell shape. The model also suggests that the orientation of mechanical and geometric cues for processes such as cell division are likely to be strongly correlated in real epithelia. Some limitations of the model in capturing geometric features of Xenopus epithelial cells are highlighted.Comment: 29 pages, 10 figures, revisio

UML Assisted Visual Debugging for Distributed Systems

The DOD is developing a Joint Battlespace Infosphere, linking a large number of data sources and user applications. To assist in this process, debugging and analysis tools are required. Software debugging is an extremely difficult cognitive process requiring comprehension of the overall application behavior, along with detailed understanding of specific application components. This is further complicated with distributed systems by the addition of other programs, their large size and synchronization issues. Typical debuggers provide inadequate support for this process, focusing primarily on the details accessible through source code. To overcome this deficiency, this research links the dynamic program execution state to a Unified Modeling Language (UML) class diagram that is reverse-engineered from data accessed within the Java Platform Debug Architecture. This research uses focus + context, graph layout, and color encoding techniques to enhance the standard UML diagram. These techniques organize and present objects and events in a manner that facilitates analysis of system behavior. High-level abstractions commonly used in system design support debugging while maintaining access to low-level details with an interactive display. The user is also able to monitor the control flow through highlighting of the relevant object and method in the display

Generating graphical and projectional editors

En ingénierie dirigée par les modèles, les langages spécifiques au domaine (DSL) offrent des notations adaptées à un domaine précis pour représenter ses différents concepts. De nombreux outils permettent la définition de DSLs en explicitant les relations entre un concept et ses représentations. En fonction de la sémantique du domaine, l’ingénieur du langage peut choisir entre des notations textuelles ou graphiques. Les langages de modélisation graphique nécessitent une gestion de la position, la taille et la disposition des éléments visuels afin de maximiser leur expressivité visuelle. La plupart des éditeurs de modélisation manquent de support automatique pour gérer ces propriétés de la syntaxe concrète. Les éditeurs projectionnels permettent aux utilisateurs de se concentrer sur la conception de leur modèle en limitant les modifications de la syntaxe concrète. Cependant, bien qu’ils offrent de multiples notations, ces éditeurs ne permettent pas la création de langage graphique. Dans ce mémoire, nous proposons une nouvelle approche pour concevoir des éditeurs graphiques et projectionnels. Nous avons créé une extension d’un éditeur projectionnel orienté vers le web, Gentleman, qui nous a permis d’extraire différentes exigences. Au cours du mémoire, nous décrivons leurs impacts sur les projections et proposons des lignes directrices ainsi que des exemples d’implémentation. Comme l’édition projectionnelle demande une gestion spécifique de l’interaction, nous présentons différentes approches pour interagir avec les représentations graphiques utilisant les nouvelles informations disponibles dans les projections. Étant donné que la plupart des exigences se concentrent sur la disposition des projections, nous avons défini plusieurs algorithmes simples de disposition qui couvrent une large gamme de structures pouvant être retrouvées dans un éditeur graphique. Enfin, afin d’évaluer cette approche, nous avons exploré la génération de trois éditeurs graphiques et projectionnels pour différents domaines: les machines d’états, les diagrammes de séquences et les partitions de musique.In model-driven engineering, domain specific-languages (DSL) provide tailored notations towards a specific problem domain to represent its different concepts. Multiple tools allow the definition of DSL by specifying the relations between a concept and its representations. Depending on the semantics of the domain, the language engineer can choose between textual or graphical notations. Graphical modeling languages require proper management of position, size, and layout to maximize their visual expressiveness. Most modeling editors lack automated support to manage these graphical concrete syntax properties. It is a time-consuming effort that affects the understandability of the model. Projectional editors prevent end-users from modifying the concrete syntax so they can focus on the modeling task. However, while they offer multiple notations, these editors lack support for graphical languages. During this thesis, we propose a new approach to design graphical and projectional editors. We created an extension of a web-oriented projectional editor, Gentleman, that allowed us to extract different requirements. During the thesis, we describe their impact on the projections and propose guidelines and examples of implementation. Because projectional editing requires specific management of the interaction, we present multiple approaches to interact with the graphical representations, using the new information available in the graphics. Since most of the requirements were focusing on the disposition of the projection, we define multiple simple layout algorithms that cover a large range of structures that can be found in a graphical editor. Finally, we explore the generation of three graphical and projectional editors for different domains: statecharts, sequence diagrams, and music sheet

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

A Smart Waste Management System Framework Using IoT and LoRa for Green City Project

Waste management is a pressing concern for society, requiring substantial labor resources and impacting various social aspects. Green cities strive for achieving a net zero-carbon footprint, including efficient waste management. The waste management system deals with three problems that are interrelated: a) the timely checking of the status of bins to prevent overflow; b) checking the precise location of bins; and c) finding the optimal route to the filled bins. The existing systems fail to satisfy all three problem areas with a single solution. To track the overflow of the bin, the proposed model uses ultrasonic sensors, which are complemented with LoRa to transmit the exact location of the bins in a real-time environment. The existing models are not that efficient at calculating the exact bin-filled status along with the precise location of the bins. The Floyd-Warshall algorithm in the proposed model optimizes waste collection using the Floyd-Warshall algorithm to determine the shortest path. Leveraging low-cost IoT technologies, specifically LoRa modules for data transfer, our solution offers benefits such as simplicity, affordability, and ease of replacement. By employing the Floyd-Warshall algorithm with a time complexity of O (n^3), our method efficiently determines the most optimal waste pickup route, saving time and resources. This study presents a smart waste management solution utilising Arduino UNO microcontrollers, ultrasonic sensors, and LoRaWAN to measure waste levels accurately. The proposed strategy aims to create clean and pollution-free cities by addressing the problem of waste distribution caused by poor collection techniques

Realistic rendering of a multi-layered human body model

Cataloged from PDF version of article.In this thesis study, a framework is proposed and implemented for the realistic rendering of a multi-layered human body model while it is moving. The proposed human body model is composed of three layers: a skeleton layer, a muscle layer, and a skin layer. The skeleton layer, represented by a set of joints and bones, controls the animation of the human body model using inverse kinematics. Muscles are represented by action lines, which are defined by a set of control points. The action line expresses the force produced by a muscle on the bones and on the skin mesh. The skin layer is modeled in a 3D modeler and deformed during animation by binding the skin layer to both the skeleton layer and the muscle layer. The skin is deformed by a two-step algorithm according to the current state of the skeleton and muscle layers. In the first step, the skin is deformed by a variant of the skinning algorithm, which deforms the skin based on the motion of the skeleton. In the second step, the skin is deformed by the underlying muscular layer. Visual results produced by the implementation is also presented. Performance experiments show that it is possible to obtain real-time frame rates for a moderately complex human model containing approximately 33,000 triangles on the skin layerYeşil, Mehmet ŞahinM.S

Visual Debugging of Object-Oriented Systems with the Unified Modeling Language

The Department of Defense (DoD) is developing a Joint Battlespace Infosphere, linking a large number of data sources and user applications. Debugging and analysis tools are required to aid in this process. Debugging of large object-oriented systems is a difficult cognitive process that requires understanding of both the overall and detailed behavior of the application. In addition, many such applications linked through a distributed system add to this complexity. Standard debuggers do not utilize visualization techniques, focusing mainly on information extracted directly from the source code. To overcome this deficiency, this research designs and implements a methodology that enables developers to analyze, troubleshoot and evaluate object-oriented systems using visualization techniques. It uses the standard UML class diagram coupled with visualization features such as focus+context, animation, graph layout, color encoding and filtering techniques to organize and present information in a manner that facilitates greater program and system comprehension. Multiple levels of abstraction, from low-level details such as source code and variable information to high-level structural detail in the form of a UML class diagram are accessible along with views of the program s control flow. The methods applied provide a considerable improvement (up to 1110%) in the number of classes that can be displayed in a set display area while still preserving user context and the semantics of UML, thus maintaining system understanding. Usability tests validated the application in terms of three criteria software visualization, debugging, and general system usability

Survey on model-based manipulation planning of deformable objects

A systematic overview on the subject of model-based manipulation planning of deformable objects is presented. Existing modelling techniques of volumetric, planar and linear deformable objects are described, emphasizing the different types of deformation. Planning strategies are categorized according to the type of manipulation goal: path planning, folding/unfolding, topology modifications and assembly. Most current contributions fit naturally into these categories, and thus the presented algorithms constitute an adequate basis for future developments.Preprin