ScaleTrotter: Illustrative Visual Travels Across Negative Scales

We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data

Fossil clitellate annelid cocoons and their microbiological inclusions from the Eocene of Seymour Island, Antarctica

Clitellate annelids have a meagre body fossil record but they secrete proteinaceous cocoons for the protection of eggs that, after hardening, are readily fossilized and offer a largely untapped resource for assessing the evolutionary history of this group. We describe three species of clitellate cocoons (viz., Burejospermum seymourense sp. nov., B. punctatum sp. nov. and Pegmatothylakos manumii gen. et sp. nov.) from the lower Eocene La Meseta Formation, Seymour Island, Antarctica. The cocoons probably derive from continental settings and were transported to, and preserved within, nearshore marine to estuarine environments. The cocoons provide the first evidence of commensal or parasitic relationships in the Eocene continental ecosystemsof Antarctica. Moreover, numerous micro-organisms and the oldest fossilizedexamples of animal spermatozoa are preserved as moulds within the consolidatedwalls of the cocoons. Fossil annelid cocoons offer potential for enhanced palaeoenvironmental interpretation of sediments, correlation between continental and shallowmarine strata, and improved understanding of the development of clitellate annelid reproductive traits and the evolutionary history of soft-bodied micro-organisms in general.Facultad de Ciencias Naturales y Muse

Face

The face is probably the part of the body, which most distinguishes us as individuals. It plays a very important role in many functions, such as speech, mastication, and expression of emotion. In the face, there is a tight coupling between different complex structures, such as skin, fat, muscle, and bone. Biomechanically driven models of the face provide an opportunity to gain insight into how these different facial components interact. The benefits of this insight are manifold, including improved maxillofacial surgical planning, better understanding of speech mechanics, and more realistic facial animations. This chapter provides an overview of facial anatomy followed by a review of previous computational models of the face. These models include facial tissue constitutive relationships, facial muscle models, and finite element models. We also detail our efforts to develop novel general and subject-specific models. We present key results from simulations that highlight the realism of the face models

Modified mass-spring system for physically based deformation modeling

Mass-spring systems are considered the simplest and most intuitive of all deformable models. They are computationally efficient, and can handle large deformations with ease. But they suffer several intrinsic limitations. In this book a modified mass-spring system for physically based deformation modeling that addresses the limitations and solves them elegantly is presented. Several implementations in modeling breast mechanics, heart mechanics and for elastic images registration are presented

Modified mass-spring system for physically based deformation modeling

Mass-spring systems are considered the simplest and most intuitive of all deformable models. They are computationally efficient, and can handle large deformations with ease. But they suffer several intrinsic limitations. In this book a modified mass-spring system for physically based deformation modeling that addresses the limitations and solves them elegantly is presented. Several implementations in modeling breast mechanics, heart mechanics and for elastic images registration are presented

Fossil clitellate annelid cocoons and their microbiological inclusions from the Eocene of Seymour Island, Antarctica

Clitellate annelids have a meagre body fossil record but they secrete proteinaceous cocoons for the protection of eggs that, after hardening, are readily fossilized and offer a largely untapped resource for assessing the evolutionary history of this group. We describe three species of clitellate cocoons (viz., Burejospermum seymourense sp. nov., B. punctatum sp. nov. and Pegmatothylakos manumii gen. et sp. nov.) from the lower Eocene La Meseta Formation, Seymour Island, Antarctica. The cocoons probably derive from continental settings and were transported to, and preserved within, nearshore marine to estuarine environments. The cocoons provide the first evidence of commensal or parasitic relationships in the Eocene continental ecosystemsof Antarctica. Moreover, numerous micro-organisms and the oldest fossilizedexamples of animal spermatozoa are preserved as moulds within the consolidatedwalls of the cocoons. Fossil annelid cocoons offer potential for enhanced palaeoenvironmental interpretation of sediments, correlation between continental and shallowmarine strata, and improved understanding of the development of clitellate annelid reproductive traits and the evolutionary history of soft-bodied micro-organisms in general.Facultad de Ciencias Naturales y Muse

Teaching the Cellular and Molecular Basis of Breast Cancer Metastasis: A Novel Workflow for Incorporating Time-lapse Microscopy Data into 3D Animation

Time-lapse confocal microscopy and organotypic 3D culture allow biologists to capture 3D movies of cells moving in real time. The Ewald Lab at Johns Hopkins School of Medicine developed this method to determine how molecular variables affect the growth of breast cancer tumors and cells’ ability to metastasize. The results support a new model of breast cancer metastasis, called Collective Epithelial Metastasis (CEM). Existing visuals of CEM are limited to microscopy and schematic model figures. Although informative to biologists, these are not intuitive to non-specialist audiences such as patient advocates and research investors. There is a need for visuals that explain the molecular and cellular basis of CEM within an anatomical context, and make conclusions of complex research more accessible. The animation teaches the role of two proteins, E-cadherin and Keratin-14, during collective invasion and dissemination. The visual challenge was to contextualize molecular concepts for an audience that first needs introduction to mammary gland anatomy, histology, and epithelial cancer definitions. Learning objectives, a script, and twenty-four page partial-color storyboard were created to teach these concepts in an appropriate level of detail. A website was developed to display the animation and provide additional information and citations. The technical project goal was to incorporate the Ewald Lab’s time-lapse microscopy datasets into an educational animation. Selected datasets show cellular events that correspond to storyboarded scenes. Volumetric data was converted into 3D surface meshes in Bitplane Imaris and imported into MAXON Cinema 4D with an OBJ Sequence Importer plugin. In Cinema 4D, the “re-animated” surface meshes were modified before being merged into a scene of the mammary duct microenvironment. Other data-derived 3D models created for the animation include: 1) breast anatomy and a metastatic tumor, segmented from DICOM data and 2) a ductal tree created in Cinema 4D, based on mouse mammary tissue. This project demonstrates that 3D time-lapse microscopy datasets can be incorporated into Cinema 4D and blend within the built anatomical and histological scene. The merging of data-derived animation with artist-created animation can improve scientific communication to audiences outside of cell biology